WorldWideScience

Sample records for base sequence effects

  1. Parallax Effect Free Mosaicing of Underwater Video Sequence Based on Texture Features

    Directory of Open Access Journals (Sweden)

    Nagaraja S

    2014-10-01

    Full Text Available In this paper, we present feature-based technique for construction of mosaic image from underwater video sequence, which suffers from parallax distortion due to propagation properties of light in the underwater environment. The most of the available mosaic tools and underwater image mosaicing techniques yields final result with some artifacts such as blurring, ghosting and seam due to presence of parallax in the input images. The removal of parallax from input images may not reduce its effects instead it must be corrected in successive steps of mosaicing. Thus, our approach minimizes the parallax effects by adopting an efficient local alignment technique after global registration. We extract texture features using Centre Symmetric Local Binary Pattern (CS-LBP descriptor in order to find feature correspondences, which are used further for estimation of homography through RANSAC. In order to increase the accuracy of global registration, we perform preprocessing such as colour alignment between two selected frames based on colour distribution adjustment. Because of existence of 100% overlap in consecutive frames of underwater video, we select frames with minimum overlap based on mutual offset in order to reduce the computation cost during mosaicing. Our approach minimizes the parallax effects considerably in final mosaic constructed using our own underwater video sequences.

  2. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

    Indian Academy of Sciences (India)

    Surjit B Dixit; Mihaly Mezei; David L Beveridge

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute–solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interactmore strongly with watermolecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning’s counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 Å from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general

  3. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies.

    Directory of Open Access Journals (Sweden)

    Patrick D Schloss

    Full Text Available The advent of next generation sequencing has coincided with a growth in interest in using these approaches to better understand the role of the structure and function of the microbial communities in human, animal, and environmental health. Yet, use of next generation sequencing to perform 16S rRNA gene sequence surveys has resulted in considerable controversy surrounding the effects of sequencing errors on downstream analyses. We analyzed 2.7×10(6 reads distributed among 90 identical mock community samples, which were collections of genomic DNA from 21 different species with known 16S rRNA gene sequences; we observed an average error rate of 0.0060. To improve this error rate, we evaluated numerous methods of identifying bad sequence reads, identifying regions within reads of poor quality, and correcting base calls and were able to reduce the overall error rate to 0.0002. Implementation of the PyroNoise algorithm provided the best combination of error rate, sequence length, and number of sequences. Perhaps more problematic than sequencing errors was the presence of chimeras generated during PCR. Because we knew the true sequences within the mock community and the chimeras they could form, we identified 8% of the raw sequence reads as chimeric. After quality filtering the raw sequences and using the Uchime chimera detection program, the overall chimera rate decreased to 1%. The chimeras that could not be detected were largely responsible for the identification of spurious operational taxonomic units (OTUs and genus-level phylotypes. The number of spurious OTUs and phylotypes increased with sequencing effort indicating that comparison of communities should be made using an equal number of sequences. Finally, we applied our improved quality-filtering pipeline to several benchmarking studies and observed that even with our stringent data curation pipeline, biases in the data generation pipeline and batch effects were observed that could potentially

  4. The effects of diffusion on an exonuclease/nanopore-based DNA sequencing engine

    OpenAIRE

    Reiner, Joseph E.; Balijepalli, Arvind; Robertson, Joseph W. F.; Drown, Bryon S.; Burden, Daniel L.; Kasianowicz, John J.

    2012-01-01

    Over 15 years ago, the ability to electrically detect and characterize individual polynucleotides as they are driven through a single protein ion channel was suggested as a potential method for rapidly sequencing DNA, base-by-base, in a ticker tape-like fashion. More recently, a variation of this method was proposed in which a nanopore would instead detect single nucleotides cleaved sequentially by an exonuclease enzyme in close proximity to one pore entrance. We analyze the exonuclease/nanop...

  5. Optimization of dynamic economic dispatch with valve-point effect using chaotic sequence based differential evolution algorithms

    International Nuclear Information System (INIS)

    A chaotic sequence based differential evolution (DE) approach for solving the dynamic economic dispatch problem (DEDP) with valve-point effect is presented in this paper. The proposed method combines the DE algorithm with the local search technique to improve the performance of the algorithm. DE is the main optimizer, while an approximated model for local search is applied to fine tune in the solution of the DE run. To accelerate convergence of DE, a series of constraints handling rules are adopted. An initial population obtained by using chaotic sequence exerts optimal performance of the proposed algorithm. The combined algorithm is validated for two test systems consisting of 10 and 13 thermal units whose incremental fuel cost function takes into account the valve-point loading effects. The proposed combined method outperforms other algorithms reported in literatures for DEDP considering valve-point effects.

  6. Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition

    Science.gov (United States)

    Littlejohn, Mathew D.; Tiplady, Kathryn; Fink, Tania A.; Lehnert, Klaus; Lopdell, Thomas; Johnson, Thomas; Couldrey, Christine; Keehan, Mike; Sherlock, Richard G.; Harland, Chad; Scott, Andrew; Snell, Russell G.; Davis, Stephen R.; Spelman, Richard J.

    2016-01-01

    The mammary gland is a prolific lipogenic organ, synthesising copious amounts of triglycerides for secretion into milk. The fat content of milk varies widely both between and within species, and recent independent genome-wide association studies have highlighted a milk fat percentage quantitative trait locus (QTL) of large effect on bovine chromosome 5. Although both EPS8 and MGST1 have been proposed to underlie these signals, the causative status of these genes has not been functionally confirmed. To investigate this QTL in detail, we report genome sequence-based imputation and association mapping in a population of 64,244 taurine cattle. This analysis reveals a cluster of 17 non-coding variants spanning MGST1 that are highly associated with milk fat percentage, and a range of other milk composition traits. Further, we exploit a high-depth mammary RNA sequence dataset to conduct expression QTL (eQTL) mapping in 375 lactating cows, revealing a strong MGST1 eQTL underpinning these effects. These data demonstrate the utility of DNA and RNA sequence-based association mapping, and implicate MGST1, a gene with no obvious mechanistic relationship to milk composition regulation, as causally involved in these processes. PMID:27146958

  7. Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition.

    Science.gov (United States)

    Littlejohn, Mathew D; Tiplady, Kathryn; Fink, Tania A; Lehnert, Klaus; Lopdell, Thomas; Johnson, Thomas; Couldrey, Christine; Keehan, Mike; Sherlock, Richard G; Harland, Chad; Scott, Andrew; Snell, Russell G; Davis, Stephen R; Spelman, Richard J

    2016-01-01

    The mammary gland is a prolific lipogenic organ, synthesising copious amounts of triglycerides for secretion into milk. The fat content of milk varies widely both between and within species, and recent independent genome-wide association studies have highlighted a milk fat percentage quantitative trait locus (QTL) of large effect on bovine chromosome 5. Although both EPS8 and MGST1 have been proposed to underlie these signals, the causative status of these genes has not been functionally confirmed. To investigate this QTL in detail, we report genome sequence-based imputation and association mapping in a population of 64,244 taurine cattle. This analysis reveals a cluster of 17 non-coding variants spanning MGST1 that are highly associated with milk fat percentage, and a range of other milk composition traits. Further, we exploit a high-depth mammary RNA sequence dataset to conduct expression QTL (eQTL) mapping in 375 lactating cows, revealing a strong MGST1 eQTL underpinning these effects. These data demonstrate the utility of DNA and RNA sequence-based association mapping, and implicate MGST1, a gene with no obvious mechanistic relationship to milk composition regulation, as causally involved in these processes. PMID:27146958

  8. The effects of a microcomputer-based laboratories learning sequence on students' concepts of function in a college physics class

    Science.gov (United States)

    Cerkovnik, Richard

    This study investigated the effects of a learning sequence on students' concepts of function. This learning sequence consisted of experiences with nonlinear graphs and non-functions in a Microcomputer-Based Laboratories (MBL) augmented college physics class. The three concepts of function which this study emphasized are a student's linear concept of function, ability to realize that any function chosen to represent the relationship between variables is only one of many possible functions, and ability to distinguish between a function and a non-function, when a relationship is represented by a graph. Data sources included pretest and posttest assessments containing open-ended questions, student journals, student interviews, student summaries, and video/audio recording of classroom activities. Six learning activities employed Microcomputer-Based Laboratory (MBL) instruction integrated with educational research in mathematics on alternative concepts or difficulties that students have with functions. These six learning activities, embedded within the regular course activities, comprised the learning sequence. Results show that the learning sequence (1) provided effective learning activities for the sub-population of students who had a tendency to draw linear graphs when other graphs would be equally appropriate, resulting in their drawing more nonlinear graphs, (2) provided effective learning activities increasing most students' ability to recognize that any function, chosen to represent the relationship between variables, is only one of many possible functions, (3) provided effective learning activities enhancing students' understanding of the univalence requirement and its connection with the application of the Vertical Line Test, (4) provided effective learning activities encouraging students' utilization of an Across-time view of functions, and (5) provided effective learning activities increasing students' ability to recognize the shapes of several common

  9. Effects of Sequence Partitioning on Compression Rate

    OpenAIRE

    Alagoz, B. Baykant

    2010-01-01

    In the paper, a theoretical work is done for investigating effects of splitting data sequence into packs of data set. We proved that a partitioning of data sequence is possible to find such that the entropy rate at each subsequence is lower than entropy rate of the source. Effects of sequence partitioning on overall compression rate are argued on the bases of partitioning statistics, and then, an optimization problem for an optimal partition is defined to improve overall compression rate of a...

  10. The Effect of Haptic Cues on Motor and Perceptual Based Implicit Sequence Learning

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    Dongwon eKim

    2014-03-01

    Full Text Available We introduced haptic cues to the serial reaction time (SRT sequence learning task alongside the standard visual cues to assess the relative contributions of haptic and visual stimuli to the formation of motor and perceptual memories. We used motorized keys to deliver brief pulse-like displacements to the resting fingers, expecting that the proximity and similarity of these cues to the subsequent response motor actions (finger activated key-presses would strengthen the motor memory trace in particular. We adopted the experimental protocol developed by Willingham in 1999 to explore whether haptic cues contribute differently than visual cues to the balance of motor and perceptual learning. We found that sequence learning occurs with haptic stimuli as with visual stimuli and we found that irrespective of the stimuli (visual or haptic the serial reaction time task leads to a greater amount of motor learning than perceptual learning.

  11. EFFECT OF SEQUENCE STRUCTURE ON THE THERMOTROPIC LIQUID CRYSTALLINE PROPERTIES OF POLYESTERAMIDES BASED ON DIMETHYLBENZIDINE, BISPHENOL-A AND p-TEREPHTHALYL CHLORIDE

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

    A series of thermotropic liquid crystalline polyesteramides with different sequence structure based on dimethylbenzidine (DMBD), bisphenol-A(BPA) and pterephthalyl chloride (TPC) was synthesized by changing the feeding order of monomers in low temperature solution polycondensation system. By means of NMR and a computer program the sequence structure parameters were measured. The effect of sequence structure on liquid crystalline phase transition temperature of PEAs obtained was investigated.

  12. cis sequence effects on gene expression

    Directory of Open Access Journals (Sweden)

    Jacobs Kevin

    2007-08-01

    Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

  13. Multiple Sequence Alignment Based on Chaotic PSO

    Science.gov (United States)

    Lei, Xiu-Juan; Sun, Jing-Jing; Ma, Qian-Zhi

    This paper introduces a new improved algorithm called chaotic PSO (CPSO) based on the thought of chaos optimization to solve multiple sequence alignment. For one thing, the chaotic variables are generated between 0 and 1 when initializing the population so that the particles are distributed uniformly in the solution space. For another thing, the chaotic sequences are generated using the Logistic mapping function in order to make chaotic search and strengthen the diversity of the population. The simulation results of several benchmark data sets of BAliBase show that the improved algorithm is effective and has good performances for the data sets with different similarity.

  14. Effects of coal ash pollution on the genetic diversity of Brachionus calyciflorus based on rDNA ITS sequences

    OpenAIRE

    Xinli Wen; Xianling Xiang; Xin Hu; Yinghao Xue; Yilong Xi; Gen Zhang

    2010-01-01

    In this study, rDNA ITS sequences were analyzed to compare the genetic diversity of Brachionus calyciflorus from the coal ash contaminated (Lake Hui) and two uncontaminated lakes (Lake Tingtang and Lake Fengming). The results showed that two sibling species in Brachionus calyciflorus species complex were defined in both Lake Tingtang and Lake Fengming, but only one sibling species was found in Lake Hui. The coal ash pollution decreased the number of sibling species. Based on the sequences of ...

  15. Effect of Addition Sequence during Neutralization and Precipitation on Iron-based Catalysts for High Temperature Shift Reaction

    Institute of Scientific and Technical Information of China (English)

    Li Wei; Zhu Jianhua; Mou Zhanjun

    2007-01-01

    The preparation of the iron-based catalysts promoted by cobalt with a small amount of copper and aluminum for the high temperature shift reaction (HTS) with different sequences of adding catalyst raw materials during neutralization and precipitation was investigated. XRD,BET and particle size distribution (PSD) were used to characterize the prepared catalysts. It was found that the catalyst crystals were all γ-Fe2O3,and the intermediate of the catalyst after aging was Fe3O4. The crystallographic form of the catalyst and its intermediate was not affected by the addition sequence in the neutralization and precipitation process. The results showed that the specific surface area and the particle size of the catalysts depended on the addition sequence to the mother liquor. Cobalt with a small amount of copper and aluminum could increase the specific surface area and decrease the particle size of catalysts.

  16. Echo Cancellation Research of Channel Estimation based on PN Sequence

    Directory of Open Access Journals (Sweden)

    Yongqin Zhou

    2010-11-01

    Full Text Available For the problem of estimation sequence effect on channel estimation accuracy and echo cancellation effect, this paper, based on the basic principle of echo cancellation, analyses the effect of PN sequence mechanism and the correlation on the channel estimation parameters. Comparing with using the input signal itself as the estimation sequence. With the input signal OFDM, the results of simulation and actual operation show that the method can increase both the accuracy of channel estimation and echo cancellation effect effectively.

  17. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.;

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  18. The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies.

    Directory of Open Access Journals (Sweden)

    Patrick D Schloss

    Full Text Available Pyrosequencing of PCR-amplified fragments that target variable regions within the 16S rRNA gene has quickly become a powerful method for analyzing the membership and structure of microbial communities. This approach has revealed and introduced questions that were not fully appreciated by those carrying out traditional Sanger sequencing-based methods. These include the effects of alignment quality, the best method of calculating pairwise genetic distances for 16S rRNA genes, whether it is appropriate to filter variable regions, and how the choice of variable region relates to the genetic diversity observed in full-length sequences. I used a diverse collection of 13,501 high-quality full-length sequences to assess each of these questions. First, alignment quality had a significant impact on distance values and downstream analyses. Specifically, the greengenes alignment, which does a poor job of aligning variable regions, predicted higher genetic diversity, richness, and phylogenetic diversity than the SILVA and RDP-based alignments. Second, the effect of different gap treatments in determining pairwise genetic distances was strongly affected by the variation in sequence length for a region; however, the effect of different calculation methods was subtle when determining the sample's richness or phylogenetic diversity for a region. Third, applying a sequence mask to remove variable positions had a profound impact on genetic distances by muting the observed richness and phylogenetic diversity. Finally, the genetic distances calculated for each of the variable regions did a poor job of correlating with the full-length gene. Thus, while it is tempting to apply traditional cutoff levels derived for full-length sequences to these shorter sequences, it is not advisable. Analysis of beta-diversity metrics showed that each of these factors can have a significant impact on the comparison of community membership and structure. Taken together, these results

  19. DNA Sequence Representation and Comparison Based on Quaternion Number System

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    Hsuan-T. Chang

    2012-12-01

    Full Text Available Conventional schemes for DNA sequence representation, storage, and processing areusually developed based on the character-based formats.We propose the quaternion number system for numerical representation and further processing on DNA sequences.In the proposed method, the quaternion cross-correlation operation can be used to obtain both the global and local matching/mismatching information between two DNA sequences from the depicted one-dimensional curve and two-dimensional pattern, respectively.Simulation results on various DNA sequences and the comparison result with the wellknown BLAST method are obtained to verify the effectiveness of the proposed method.

  20. Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens.

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    Oliver Deusch

    Full Text Available Previously, we demonstrated that dietary protein:carbohydrate ratio dramatically affects the fecal microbial taxonomic structure of kittens using targeted 16S gene sequencing. The present study, using the same fecal samples, applied deep Illumina shotgun sequencing to identify the diet-associated functional potential and analyze taxonomic changes of the feline fecal microbiome.Fecal samples from kittens fed one of two diets differing in protein and carbohydrate content (high-protein, low-carbohydrate, HPLC; and moderate-protein, moderate-carbohydrate, MPMC were collected at 8, 12 and 16 weeks of age (n = 6 per group. A total of 345.3 gigabases of sequence were generated from 36 samples, with 99.75% of annotated sequences identified as bacterial. At the genus level, 26% and 39% of reads were annotated for HPLC- and MPMC-fed kittens, with HPLC-fed cats showing greater species richness and microbial diversity. Two phyla, ten families and fifteen genera were responsible for more than 80% of the sequences at each taxonomic level for both diet groups, consistent with the previous taxonomic study. Significantly different abundances between diet groups were observed for 324 genera (56% of all genera identified demonstrating widespread diet-induced changes in microbial taxonomic structure. Diversity was not affected over time. Functional analysis identified 2,013 putative enzyme function groups were different (p<0.000007 between the two dietary groups and were associated to 194 pathways, which formed five discrete clusters based on average relative abundance. Of those, ten contained more (p<0.022 enzyme functions with significant diet effects than expected by chance. Six pathways were related to amino acid biosynthesis and metabolism linking changes in dietary protein with functional differences of the gut microbiome.These data indicate that feline feces-derived microbiomes have large structural and functional differences relating to the dietary

  1. Triple helices formed at oligopyrimidine*oligopurine sequences with base pair inversions: effect of a triplex-specific ligand on stability and selectivity.

    OpenAIRE

    Kukreti, S; Sun, J S; Loakes, D; Brown, D M; Nguyen, C. H.; Bisagni, E.; Garestier, T; Helene, C

    1998-01-01

    Oligonucleotide-directed triple helix formation is mostly restricted to oligopyrimidine*oligopurine sequences of double helical DNA. An interruption of one or two pyrimidines in the oligopurine target strand leads to a strong triplex destabilisation. We have investigated the effect of nucleotide analogues introduced in the third strand at the site opposite the base pair inversion(s). We show that a 3-nitropyrrole derivative (M) discriminates G*C from C*G, A*T and T*A in the presence of a trip...

  2. The Effect of a Classroom-Based Intensive Robotics and Programming Workshop on Sequencing Ability in Early Childhood

    Science.gov (United States)

    Kazakoff, Elizabeth R.; Sullivan, Amanda; Bers, Marina U.

    2013-01-01

    This paper examines the impact of programming robots on sequencing ability during a 1-week intensive robotics workshop at an early childhood STEM magnet school in the Harlem area of New York City. Children participated in computer programming activities using a developmentally appropriate tangible programming language CHERP, specifically designed…

  3. SNAD: sequence name annotation-based designer

    Directory of Open Access Journals (Sweden)

    Gorbalenya Alexander E

    2009-08-01

    Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

  4. Secondary-task effects on sequence learning.

    Science.gov (United States)

    Heuer, H; Schmidtke, V

    1996-01-01

    With a repeated sequence of stimuli, performance in a serial reaction-time task improves more than with a random sequence. The difference has been taken as a measure of implicit sequence learning. Implicit sequence learning is impaired when a secondary task is added to the serial RT task. In the first experiment, secondary-task effects on different types of sequences were studied to test the hypothesis that the learning of unique sequences (where each sequence element has a unique relation to the following one) is not impaired by the secondary task, while the learning of ambiguous sequences is. The sequences were random up to a certain order of sequential dependencies, where they became deterministic. Contrary to the hypothesis, secondary-task effects on the learning of unique sequences were as strong or stronger than such effects on the learning of ambiguous sequences. In the second experiment a hybrid sequence (with unique as well as ambiguous transitions) was used with different secondary tasks. A visuo-spatial and a verbal memory task did not interfere with the learning of the sequence, but interference was observed with an auditory go/no-go task in which high- and low-pitched tones were presented after each manual response and a foot pedal had to be pressed in response to high-pitched tones. Thus, interference seems to be specific to certain secondary tasks and may be related to memory processes (but most likely not to visuo-spatial and verbal memory) or to the organizations of sequences, consistent with previous suggestions. PMID:8810586

  5. Microsatellite Length Scoring by Single Molecule Real Time Sequencing - Effects of Sequence Structure and PCR Regime.

    Science.gov (United States)

    Liljegren, Mikkel Meyn; de Muinck, Eric Jacques; Trosvik, Pål

    2016-01-01

    Microsatellites are DNA sequences consisting of repeated, short (1-6 bp) sequence motifs that are highly mutable by enzymatic slippage during replication. Due to their high intrinsic variability, microsatellites have important applications in population genetics, forensics, genome mapping, as well as cancer diagnostics and prognosis. The current analytical standard for microsatellites is based on length scoring by high precision electrophoresis, but due to increasing efficiency next-generation sequencing techniques may provide a viable alternative. Here, we evaluated single molecule real time (SMRT) sequencing, implemented in the PacBio series of sequencing apparatuses, as a means of microsatellite length scoring. To this end we carried out multiplexed SMRT sequencing of plasmid-carried artificial microsatellites of varying structure under different pre-sequencing PCR regimes. For each repeat structure, reads corresponding to the target length dominated. We found that pre-sequencing amplification had large effects on scoring accuracy and error distribution relative to controls, but that the effects of the number of amplification cycles were generally weak. In line with expectations enzymatic slippage decreased proportionally with microsatellite repeat unit length and increased with repetition number. Finally, we determined directional mutation trends, showing that PCR and SMRT sequencing introduced consistent but opposing error patterns in contraction and expansion of the microsatellites on the repeat motif and single nucleotide level. PMID:27414800

  6. Microsatellite Length Scoring by Single Molecule Real Time Sequencing - Effects of Sequence Structure and PCR Regime.

    Directory of Open Access Journals (Sweden)

    Mikkel Meyn Liljegren

    Full Text Available Microsatellites are DNA sequences consisting of repeated, short (1-6 bp sequence motifs that are highly mutable by enzymatic slippage during replication. Due to their high intrinsic variability, microsatellites have important applications in population genetics, forensics, genome mapping, as well as cancer diagnostics and prognosis. The current analytical standard for microsatellites is based on length scoring by high precision electrophoresis, but due to increasing efficiency next-generation sequencing techniques may provide a viable alternative. Here, we evaluated single molecule real time (SMRT sequencing, implemented in the PacBio series of sequencing apparatuses, as a means of microsatellite length scoring. To this end we carried out multiplexed SMRT sequencing of plasmid-carried artificial microsatellites of varying structure under different pre-sequencing PCR regimes. For each repeat structure, reads corresponding to the target length dominated. We found that pre-sequencing amplification had large effects on scoring accuracy and error distribution relative to controls, but that the effects of the number of amplification cycles were generally weak. In line with expectations enzymatic slippage decreased proportionally with microsatellite repeat unit length and increased with repetition number. Finally, we determined directional mutation trends, showing that PCR and SMRT sequencing introduced consistent but opposing error patterns in contraction and expansion of the microsatellites on the repeat motif and single nucleotide level.

  7. Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition

    OpenAIRE

    Littlejohn, Mathew D; Tiplady, Kathryn; Tania A. Fink; Lehnert, Klaus; Lopdell, Thomas; Johnson, Thomas; Couldrey, Christine; Keehan, Mike; Richard G. Sherlock; Harland, Chad; Scott, Andrew; Russell G. Snell; Davis, Stephen R.; Spelman, Richard J.

    2016-01-01

    The mammary gland is a prolific lipogenic organ, synthesising copious amounts of triglycerides for secretion into milk. The fat content of milk varies widely both between and within species, and recent independent genome-wide association studies have highlighted a milk fat percentage quantitative trait locus (QTL) of large effect on bovine chromosome 5. Although both EPS8 and MGST1 have been proposed to underlie these signals, the causative status of these genes has not been functionally conf...

  8. Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems▿

    OpenAIRE

    Nowrousian, Minou

    2010-01-01

    Over the past 5 years, large-scale sequencing has been revolutionized by the development of several so-called next-generation sequencing (NGS) technologies. These have drastically increased the number of bases obtained per sequencing run while at the same time decreasing the costs per base. Compared to Sanger sequencing, NGS technologies yield shorter read lengths; however, despite this drawback, they have greatly facilitated genome sequencing, first for prokaryotic genomes and within the las...

  9. A repetitive sequence assembler based on next-generation sequencing.

    Science.gov (United States)

    Lian, S; Tu, Y; Wang, Y; Chen, X; Wang, L

    2016-01-01

    Repetitive sequences of variable length are common in almost all eukaryotic genomes, and most of them are presumed to have important biomedical functions and can cause genomic instability. Next-generation sequencing (NGS) technologies provide the possibility of identifying capturing these repetitive sequences directly from the NGS data. In this study, we assessed the performances in identifying capturing repeats of leading assemblers, such as Velvet, SOAPdenovo, SGA, MSR-CA, Bambus2, ALLPATHS-LG, and AByss using three real NGS datasets. Our results indicated that most of them performed poorly in capturing the repeats. Consequently, we proposed a repetitive sequence assembler, named NGSReper, for capturing repeats from NGS data. Simulated datasets were used to validate the feasibility of NGSReper. The results indicate that the completeness of capturing repeat is up to 99%. Cross validation was performed in three real NGS datasets, and extensive comparisons indicate that NGSReper performed best in terms of completeness and accuracy in capturing repeats. In conclusion, NGSReper is an appropriate and suitable tool for capturing repeats directly from NGS data. PMID:27525861

  10. AbCD: arbitrary coverage design for sequencing-based genetic studies

    OpenAIRE

    Kang, Jian; Huang, Kuan-Chieh; Xu, Zheng; Wang, Yunfei; Abecasis, Gonçalo R.; Li, Yun

    2013-01-01

    Summary: Recent advances in sequencing technologies have revolutionized genetic studies. Although high-coverage sequencing can uncover most variants present in the sequenced sample, low-coverage sequencing is appealing for its cost effectiveness. Here, we present AbCD (arbitrary coverage design) to aid the design of sequencing-based studies. AbCD is a user-friendly interface providing pre-estimated effective sample sizes, specific to each minor allele frequency category, for designs with arbi...

  11. Multiple Base Substitution Corrections in DNA Sequence Evolution

    Science.gov (United States)

    Kowalczuk, M.; Mackiewicz, P.; Szczepanik, D.; Nowicka, A.; Dudkiewicz, M.; Dudek, M. R.; Cebrat, S.

    We discuss the Jukes and Cantor's one-parameter model and Kimura's two-parameter model unability to describe evolution of asymmetric DNA molecules. The standard distance measure between two DNA sequences, which is the number of substitutions per site, should include the effect of multiple base substitutions separately for each type of the base. Otherwise, the respective tables of substitutions cannot reconstruct the asymmetric DNA molecule with respect to the composition. Basing on Kimura's neutral theory, we have derived a linear law for the correlation of the mean survival time of nucleotides under constant mutation pressure and their fraction in the genome. According to the law, the corrections to Kimura's theory have been discussed to describe evolution of genomes with asymmetric nucleotide composition. We consider the particular case of the strongly asymmetric Borrelia burgdorferi genome and we discuss in detail the corrections, which should be introduced into the distance measure between two DNA sequences to include multiple base substitutions.

  12. Chip-based sequencing nucleic acids

    Science.gov (United States)

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  13. Skeleton-based human action recognition using multiple sequence alignment

    Science.gov (United States)

    Ding, Wenwen; Liu, Kai; Cheng, Fei; Zhang, Jin; Li, YunSong

    2015-05-01

    Human action recognition and analysis is an active research topic in computer vision for many years. This paper presents a method to represent human actions based on trajectories consisting of 3D joint positions. This method first decompose action into a sequence of meaningful atomic actions (actionlets), and then label actionlets with English alphabets according to the Davies-Bouldin index value. Therefore, an action can be represented using a sequence of actionlet symbols, which will preserve the temporal order of occurrence of each of the actionlets. Finally, we employ sequence comparison to classify multiple actions through using string matching algorithms (Needleman-Wunsch). The effectiveness of the proposed method is evaluated on datasets captured by commodity depth cameras. Experiments of the proposed method on three challenging 3D action datasets show promising results.

  14. Steganalytic method based on short and repeated sequence distance statistics

    Institute of Scientific and Technical Information of China (English)

    WANG GuoXin; PING XiJian; XU ManKun; ZHANG Tao; BAO XiRui

    2008-01-01

    According to the distribution characteristics of short and repeated sequence (SRS),a steganalytic method based on the correlation of image bit planes is proposed.Firstly,we provide the conception of SRS distance statistics and deduce its statistical distribution.Because the SRS distance statistics can effectively reflect the correlation of the sequence,SRS has statistical features when the image bit plane sequence equals the image width.Using this characteristic,the steganalytic method is fulfilled by the distinct test of Poisson distribution.Experimental results show a good performance for detecting LSB matching steganographic method in still images.By the way,the proposed method is not designed for specific steganographic algorithms and has good generality.

  15. Solid-State Nanopore-Based DNA Sequencing Technology

    Directory of Open Access Journals (Sweden)

    Zewen Liu

    2016-01-01

    Full Text Available The solid-state nanopore-based DNA sequencing technology is becoming more and more attractive for its brand new future in gene detection field. The challenges that need to be addressed are diverse: the effective methods to detect base-specific signatures, the control of the nanopore’s size and surface properties, and the modulation of translocation velocity and behavior of the DNA molecules. Among these challenges, the realization of the high-quality nanopores with the help of modern micro/nanofabrication technologies is a crucial one. In this paper, typical technologies applied in the field of solid-state nanopore-based DNA sequencing have been reviewed.

  16. Effects of impregnation sequence on the microstructure and performances of Cu-Co based catalysts for the synthesis of higher alcohols

    Institute of Scientific and Technical Information of China (English)

    Siyu Deng; Wei Chu; Huiyuan Xu; Limin Shi; Lihong Huang

    2008-01-01

    Silica-supported CuCo catalysts were prepared by impregnation method with different impregnation sequence for higher alcohols synthesis. These catalysts were characterized by H2-TPR, XRD, N2 adsorption, XPS techniques and CO selective hydrogenation reaction measurement. The effects of impregnation sequence on the structure and performance of cata-lysts were investigated, and there were important influences on the selectivity to higher alcohols. There was a strong synergistic effect between copper and cobalt for the co-impregnated sample. The CuCo/SiO2 catalyst prepared by co-impregnation showed a better yield of total alcohols, and a higher selectivity to total alcohols which reached 51.5%.

  17. Numerical Characterization of DNA Sequence Based on Dinucleotides

    OpenAIRE

    Xingqin Qi; Edgar Fuller; Qin Wu; Cun-Quan Zhang

    2012-01-01

    Sequence comparison is a primary technique for the analysis of DNA sequences. In order to make quantitative comparisons, one devises mathematical descriptors that capture the essence of the base composition and distribution of the sequence. Alignment methods and graphical techniques (where each sequence is represented by a curve in high-dimension Euclidean space) have been used popularly for a long time. In this contribution we will introduce a new nongraphical and nonalignment approach based...

  18. Effect of dephasing on DNA sequencing via transverse electronic transport

    Energy Technology Data Exchange (ETDEWEB)

    Zwolak, Michael [Los Alamos National Laboratory; Krems, Matt [NON LANL; Pershin, Yuriy V [NON LANL; Di Ventra, Massimiliano [NON LANL

    2009-01-01

    We study theoretically the effects of dephasing on DNA sequencing in a nanopore via transverse electronic transport. To do this, we couple classical molecular dynamics simulations with transport calculations using scattering theory. Previous studies, which did not include dephasing, have shown that by measuring the transverse current of a particular base multiple times, one can get distributions of currents for each base that are distinguishable. We introduce a dephasing parameter into transport calculations to simulate the effects of the ions and other fluctuations. These effects lower the overall magnitude of the current, but have little effect on the current distributions themselves. The results of this work further implicate that distinguishing DNA bases via transverse electronic transport has potential as a sequencing tool.

  19. Movement Pattern Analysis Based on Sequence Signatures

    Directory of Open Access Journals (Sweden)

    Seyed Hossein Chavoshi

    2015-09-01

    Full Text Available Increased affordability and deployment of advanced tracking technologies have led researchers from various domains to analyze the resulting spatio-temporal movement data sets for the purpose of knowledge discovery. Two different approaches can be considered in the analysis of moving objects: quantitative analysis and qualitative analysis. This research focuses on the latter and uses the qualitative trajectory calculus (QTC, a type of calculus that represents qualitative data on moving point objects (MPOs, and establishes a framework to analyze the relative movement of multiple MPOs. A visualization technique called sequence signature (SESI is used, which enables to map QTC patterns in a 2D indexed rasterized space in order to evaluate the similarity of relative movement patterns of multiple MPOs. The applicability of the proposed methodology is illustrated by means of two practical examples of interacting MPOs: cars on a highway and body parts of a samba dancer. The results show that the proposed method can be effectively used to analyze interactions of multiple MPOs in different domains.

  20. Simulation-Based Evaluation of Learning Sequences for Instructional Technologies

    Science.gov (United States)

    McEneaney, John E.

    2016-01-01

    Instructional technologies critically depend on systematic design, and learning hierarchies are a commonly advocated tool for designing instructional sequences. But hierarchies routinely allow numerous sequences and choosing an optimal sequence remains an unsolved problem. This study explores a simulation-based approach to modeling learning…

  1. Semantics-based Refinement of Mandatory Behavior of Sequence Diagrams

    CERN Document Server

    Lu, Lunjin

    2010-01-01

    Sequence diagrams are a widely used design notation for describing software behaviors. Many reusable software artifacts such as design patterns and design aspects make use of sequence diagrams to describe interaction behaviors. When a pattern or an aspect is reused in an application, it is important to ensure that the sequence diagrams for the application correctly refines the corresponding sequence diagrams for the pattern or aspect. Reasoning about refinement of sequence diagrams has not been addressed adequately in literature. In this paper, we focus on refinement of mandatory behavior specified by a UML sequence diagram. A novel trace semantics is given that captures precisely mandatory behavior specified by a sequence diagram and a refinement relation between sequence diagrams is formalized based on the semantics. Properties of the trace semantics and the refinement relation are studied.

  2. Watermarking scheme of colour image based on chaotic sequences

    Institute of Scientific and Technical Information of China (English)

    LIU Nian-sheng; GUO Dong-hui

    2009-01-01

    The proposed perceptual mask is based on the singularity of cover image and matches very well with the properties of the human visual system. The cover colour image is decomposed into several subbands by the wavelet transform. The water-mark composed of chaotic sequence and the covert image is embedded into the subband with the largest energy. The chaos system plays an important role in the security invisibility and robustness of the proposed scheme. The parameter and initial state of chaos system can directly influence the generation of watermark information as a key. Moreover, the watermark information has the property of spread spectrum signal by chaotic sequence to improve the invisibility and security of watermarked image. Experimental results and comparisons with other watermarking techniques prove that the proposed algorithm is effective and feasible, and improves the security, invisibility and robustness of watermarking information.

  3. Identification of protein superfamily from structure- based sequence motif

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The structure-based sequence motif of the distant proteins in evolution, protein tyrosine phosphatases (PTP) Ⅰ and Ⅱ superfamilies, as an example, has been defined by the structural comparison, structure-based sequence alignment and analyses on substitution patterns of residues in common sequence conserved regions. And the phosphatases Ⅰ and Ⅱ can be correctly identified together by the structure-based PTP sequence motif from SWISS-PROT and TrEBML databases. The results show that the correct rates of identification are over 98%. This is the first time to identify PTP Ⅰ and Ⅱ together by this motif.

  4. Asynchronous symmetry-based sequences for homonuclear dipolar recoupling in solid-state nuclear magnetic resonance

    International Nuclear Information System (INIS)

    We show a theoretical framework, based on triple-mode Floquet theory, to analyze recoupling sequences derived from symmetry-based pulse sequences, which have a non-vanishing effective field and are not rotor synchronized. We analyze the properties of one such sequence, a homonuclear double-quantum recoupling sequence derived from the C721 sequence. The new asynchronous sequence outperforms the rotor-synchronized version for spin pairs with small dipolar couplings in the presence of large chemical-shift anisotropy. The resonance condition of the new sequence is analyzed using triple-mode Floquet theory. Analytical calculations of second-order effective Hamiltonian are performed to compare the efficiency in suppressing second-order cross terms. Experiments and numerical simulations are shown to corroborate the results of the theoretical analysis

  5. Prediction of potential drug targets based on simple sequence properties

    Directory of Open Access Journals (Sweden)

    Lai Luhua

    2007-09-01

    Full Text Available Abstract Background During the past decades, research and development in drug discovery have attracted much attention and efforts. However, only 324 drug targets are known for clinical drugs up to now. Identifying potential drug targets is the first step in the process of modern drug discovery for developing novel therapeutic agents. Therefore, the identification and validation of new and effective drug targets are of great value for drug discovery in both academia and pharmaceutical industry. If a protein can be predicted in advance for its potential application as a drug target, the drug discovery process targeting this protein will be greatly speeded up. In the current study, based on the properties of known drug targets, we have developed a sequence-based drug target prediction method for fast identification of novel drug targets. Results Based on simple physicochemical properties extracted from protein sequences of known drug targets, several support vector machine models have been constructed in this study. The best model can distinguish currently known drug targets from non drug targets at an accuracy of 84%. Using this model, potential protein drug targets of human origin from Swiss-Prot were predicted, some of which have already attracted much attention as potential drug targets in pharmaceutical research. Conclusion We have developed a drug target prediction method based solely on protein sequence information without the knowledge of family/domain annotation, or the protein 3D structure. This method can be applied in novel drug target identification and validation, as well as genome scale drug target predictions.

  6. Identifying discriminative classification-based motifs in biological sequences

    OpenAIRE

    Vens, Celine; Rosso, Marie-Noëlle; Danchin, Etienne

    2011-01-01

    Motivation: Identification of conserved motifs in biological sequences is crucial to unveil common shared functions. Many tools exist for motif identification, including some that allow degenerate positions with multiple possible nucleotides or amino acids. Most efficient methods available today search conserved motifs in a set of sequences, but do not check for their specificity regarding to a set of negative sequences. Results: We present a tool to identify degenerate motifs, based on a giv...

  7. RNA-RNA interaction prediction based on multiple sequence alignments

    CERN Document Server

    Li, Andrew X; Qin, Jing; Reidys, Christian M

    2010-01-01

    Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes for pairs of RNA sequences. These algorithms and the biological requirement of more reliable interactions motivate to utilize the additional information contained in multiple sequence alignments and to generalize the above framework to the partition function and base pairing probabilities for multiple sequence alignments.

  8. Feature-based Image Sequence Compression Coding

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A novel compressing method for video teleconference applications is presented. Semantic-based coding based on human image feature is realized, where human features are adopted as parameters. Model-based coding and the concept of vector coding are combined with the work on image feature extraction to obtain the result.

  9. An Ant-Based Model for Multiple Sequence Alignment

    CERN Document Server

    Guinand, Frédéric

    2008-01-01

    Multiple sequence alignment is a key process in today's biology, and finding a relevant alignment of several sequences is much more challenging than just optimizing some improbable evaluation functions. Our approach for addressing multiple sequence alignment focuses on the building of structures in a new graph model: the factor graph model. This model relies on block-based formulation of the original problem, formulation that seems to be one of the most suitable ways for capturing evolutionary aspects of alignment. The structures are implicitly built by a colony of ants laying down pheromones in the factor graphs, according to relations between blocks belonging to the different sequences.

  10. Nanopore-Based Target Sequence Detection.

    Science.gov (United States)

    Morin, Trevor J; Shropshire, Tyler; Liu, Xu; Briggs, Kyle; Huynh, Cindy; Tabard-Cossa, Vincent; Wang, Hongyun; Dunbar, William B

    2016-01-01

    The promise of portable diagnostic devices relies on three basic requirements: comparable sensitivity to established platforms, inexpensive manufacturing and cost of operations, and the ability to survive rugged field conditions. Solid state nanopores can meet all these requirements, but to achieve high manufacturing yields at low costs, assays must be tolerant to fabrication imperfections and to nanopore enlargement during operation. This paper presents a model for molecular engineering techniques that meets these goals with the aim of detecting target sequences within DNA. In contrast to methods that require precise geometries, we demonstrate detection using a range of pore geometries. As a result, our assay model tolerates any pore-forming method and in-situ pore enlargement. Using peptide nucleic acid (PNA) probes modified for conjugation with synthetic bulk-adding molecules, pores ranging 15-50 nm in diameter are shown to detect individual PNA-bound DNA. Detection of the CFTRΔF508 gene mutation, a codon deletion responsible for ∼66% of all cystic fibrosis chromosomes, is demonstrated with a 26-36 nm pore size range by using a size-enhanced PNA probe. A mathematical framework for assessing the statistical significance of detection is also presented. PMID:27149679

  11. Nanopore-Based Target Sequence Detection

    Science.gov (United States)

    Morin, Trevor J.; Shropshire, Tyler; Liu, Xu; Briggs, Kyle; Huynh, Cindy; Tabard-Cossa, Vincent; Wang, Hongyun; Dunbar, William B.

    2016-01-01

    The promise of portable diagnostic devices relies on three basic requirements: comparable sensitivity to established platforms, inexpensive manufacturing and cost of operations, and the ability to survive rugged field conditions. Solid state nanopores can meet all these requirements, but to achieve high manufacturing yields at low costs, assays must be tolerant to fabrication imperfections and to nanopore enlargement during operation. This paper presents a model for molecular engineering techniques that meets these goals with the aim of detecting target sequences within DNA. In contrast to methods that require precise geometries, we demonstrate detection using a range of pore geometries. As a result, our assay model tolerates any pore-forming method and in-situ pore enlargement. Using peptide nucleic acid (PNA) probes modified for conjugation with synthetic bulk-adding molecules, pores ranging 15-50 nm in diameter are shown to detect individual PNA-bound DNA. Detection of the CFTRΔF508 gene mutation, a codon deletion responsible for ∼66% of all cystic fibrosis chromosomes, is demonstrated with a 26-36 nm pore size range by using a size-enhanced PNA probe. A mathematical framework for assessing the statistical significance of detection is also presented. PMID:27149679

  12. Sequence Context Specific Mutagenesis and Base Excision Repair

    OpenAIRE

    Donigan, Katherine; Sweasy, Joann B.

    2009-01-01

    Base excision repair is critical for the maintenance of genome stability because it repairs at least 20,000 endogenously generated DNA lesions per cell per day. Several enzymes within the base excision repair pathway exhibit sequence context dependency during the excision and DNA synthesis steps of repair. New evidence is emerging that germ line and tumor-associated variants of enzymes in this repair pathway exhibit sequence context dependence that is different from their ancestral counterpar...

  13. A Diagnostic HIV-1 Tropism System Based on Sequence Relatedness

    OpenAIRE

    Edwards, Suzanne; Stucki, Heinz; Bader, Joëlle; Vidal, Vincent; Kaiser, Rolf; Battegay, Manuel; Klimkait, Thomas

    2014-01-01

    Key clinical studies for HIV coreceptor antagonists have used the phenotyping-based Trofile test. Meanwhile various simpler-to-do genotypic tests have become available that are compatible with standard laboratory equipment and Web-based interpretation tools. However, these systems typically analyze only the most prominent virus sequence in a specimen. We present a new diagnostic HIV tropism test not needing DNA sequencing. The system, XTrack, uses physical properties of DNA duplexes after hyb...

  14. Immune and Genetic Algorithm Based Assembly Sequence Planning

    Institute of Scientific and Technical Information of China (English)

    YANG Jian-guo; LI Bei-zhi; YU Lei; JIN Yu-song

    2004-01-01

    In this paper an assembly sequence planning model inspired by natural immune and genetic algorithm (ASPIG) based on the part degrees of freedom matrix (PDFM) is proposed, and a proto system - DSFAS based on the ASPIG is introduced to solve assembly sequence problem. The concept and generation of PDFM and DSFAS are also discussed. DSFAS can prevent premature convergence, and promote population diversity, and can accelerate the learning and convergence speed in behavior evolution problem.

  15. Base-sequence-dependent sliding of proteins on DNA

    OpenAIRE

    Barbi, M; Place, C.; Popkov, V.; Salerno, M.

    2004-01-01

    The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general validity and the implications of the results are discussed.

  16. DNA sequence analysis with droplet-based microfluidics

    Science.gov (United States)

    Abate, Adam R.; Hung, Tony; Sperling, Ralph A.; Mary, Pascaline; Rotem, Assaf; Agresti, Jeremy J.; Weiner, Michael A.; Weitz, David A.

    2014-01-01

    Droplet-based microfluidic techniques can form and process micrometer scale droplets at thousands per second. Each droplet can house an individual biochemical reaction, allowing millions of reactions to be performed in minutes with small amounts of total reagent. This versatile approach has been used for engineering enzymes, quantifying concentrations of DNA in solution, and screening protein crystallization conditions. Here, we use it to read the sequences of DNA molecules with a FRET-based assay. Using probes of different sequences, we interrogate a target DNA molecule for polymorphisms. With a larger probe set, additional polymorphisms can be interrogated as well as targets of arbitrary sequence. PMID:24185402

  17. Nanopore-based Fourth-generation DNA Sequencing Technology

    Institute of Scientific and Technical Information of China (English)

    Yanxiao Feng; Yuechuan Zhang; Cuifeng Ying; Deqiang Wang; Chunlei Du

    2015-01-01

    Nanopore-based sequencers, as the fourth-generation DNA sequencing technology, have the potential to quickly and reliably sequence the entire human genome for less than $1000, and possibly for even less than$100. The single-molecule techniques used by this technology allow us to further study the interaction between DNA and protein, as well as between protein and protein. Nanopore analysis opens a new door to molecular biology investigation at the single-molecule scale. In this article, we have reviewed academic achievements in nanopore technology from the past as well as the latest advances, including both biological and solid-state nanopores, and discussed their recent and potential applications.

  18. An optical CDMA system based on chaotic sequences

    Science.gov (United States)

    Liu, Xiao-lei; En, De; Wang, Li-guo

    2014-03-01

    In this paper, a coherent asynchronous optical code division multiple access (OCDMA) system is proposed, whose encoder/decoder is an all-optical generator. This all-optical generator can generate analog and bipolar chaotic sequences satisfying the logistic maps. The formula of bit error rate (BER) is derived, and the relationship of BER and the number of simultaneous transmissions is analyzed. Due to the good property of correlation, this coherent OCDMA system based on these bipolar chaotic sequences can support a large number of simultaneous users, which shows that these chaotic sequences are suitable for asynchronous OCDMA system.

  19. Analysis of Chimpanzee History Based on Genome Sequence Alignments

    OpenAIRE

    Caswell, Jennifer L.; Richter, Daniel J.; Neubauer, Julie; Schirmer, Christine; Gnerre, Sante; Mallick, Swapan; Reich, David Emil

    2008-01-01

    Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate tens of millions of base pairs of multiple sequence alignments from combinations of three western chimpanzees, three central chimpanzees, an eastern chimpanzee, a bonobo, a human, an orangutan, and a macaque. Analysis provides a more precise understanding of demographic history than was previously...

  20. Markov chaotic sequences for correlation based watermarking schemes

    International Nuclear Information System (INIS)

    In this paper, statistical analysis of watermarking schemes based on correlation detection is presented. Statistical properties of watermark sequences generated by piecewise-linear Markov maps are exploited, resulting in superior watermark detection reliability. Correlation/spectral properties of such sequences are easily controllable, a fact that affects the watermarking system performance. A family of chaotic maps, namely the skew tent map family, is proposed for use in watermarking schemes

  1. Differentially Private Frequent Sequence Mining via Sampling-based Candidate Pruning

    Science.gov (United States)

    Xu, Shengzhi; Cheng, Xiang; Li, Zhengyi; Xiong, Li

    2016-01-01

    In this paper, we study the problem of mining frequent sequences under the rigorous differential privacy model. We explore the possibility of designing a differentially private frequent sequence mining (FSM) algorithm which can achieve both high data utility and a high degree of privacy. We found, in differentially private FSM, the amount of required noise is proportionate to the number of candidate sequences. If we could effectively reduce the number of unpromising candidate sequences, the utility and privacy tradeoff can be significantly improved. To this end, by leveraging a sampling-based candidate pruning technique, we propose a novel differentially private FSM algorithm, which is referred to as PFS2. The core of our algorithm is to utilize sample databases to further prune the candidate sequences generated based on the downward closure property. In particular, we use the noisy local support of candidate sequences in the sample databases to estimate which sequences are potentially frequent. To improve the accuracy of such private estimations, a sequence shrinking method is proposed to enforce the length constraint on the sample databases. Moreover, to decrease the probability of misestimating frequent sequences as infrequent, a threshold relaxation method is proposed to relax the user-specified threshold for the sample databases. Through formal privacy analysis, we show that our PFS2 algorithm is ε-differentially private. Extensive experiments on real datasets illustrate that our PFS2 algorithm can privately find frequent sequences with high accuracy. PMID:26973430

  2. DNA sequence analysis using hierarchical ART-based classification networks

    Energy Technology Data Exchange (ETDEWEB)

    LeBlanc, C.; Hruska, S.I. [Florida State Univ., Tallahassee, FL (United States); Katholi, C.R.; Unnasch, T.R. [Univ. of Alabama, Birmingham, AL (United States)

    1994-12-31

    Adaptive resonance theory (ART) describes a class of artificial neural network architectures that act as classification tools which self-organize, work in real-time, and require no retraining to classify novel sequences. We have adapted ART networks to provide support to scientists attempting to categorize tandem repeat DNA fragments from Onchocerca volvulus. In this approach, sequences of DNA fragments are presented to multiple ART-based networks which are linked together into two (or more) tiers; the first provides coarse sequence classification while the sub- sequent tiers refine the classifications as needed. The overall rating of the resulting classification of fragments is measured using statistical techniques based on those introduced to validate results from traditional phylogenetic analysis. Tests of the Hierarchical ART-based Classification Network, or HABclass network, indicate its value as a fast, easy-to-use classification tool which adapts to new data without retraining on previously classified data.

  3. Co-barcoded sequence reads from long DNA fragments: A cost-effective solution for Perfect Genome sequencing

    Directory of Open Access Journals (Sweden)

    Brock A Peters

    2015-01-01

    Full Text Available Next generation sequencing (NGS technologies, primarily based on massively parallel sequencing (MPS, have touched and radically changed almost all aspects of research worldwide. These technologies have allowed for the rapid analysis, to date, of the genomes of more than 2,000 different species. In humans, NGS has arguably had the largest impact. Over 100,000 genomes of individual humans (based on various estimates have been sequenced allowing for deep insights into what makes individuals and families unique and what causes disease in each of us. Despite all of this progress, the current state of the art in sequence technology is far from generating a perfect genome sequence and much remains to be understood in the biology of human and other organisms’ genomes. In the article that follows we outline, why the perfect genome in humans is important, what is lacking from current human whole genome sequences, and a potential strategy for achieving the perfect genome in a cost effective manner.

  4. Evaluation of Hybridization Capture Versus Amplicon‐Based Methods for Whole‐Exome Sequencing

    Science.gov (United States)

    Samorodnitsky, Eric; Jewell, Benjamin M.; Hagopian, Raffi; Miya, Jharna; Wing, Michele R.; Lyon, Ezra; Damodaran, Senthilkumar; Bhatt, Darshna; Reeser, Julie W.; Datta, Jharna

    2015-01-01

    ABSTRACT Next‐generation sequencing has aided characterization of genomic variation. While whole‐genome sequencing may capture all possible mutations, whole‐exome sequencing remains cost‐effective and captures most phenotype‐altering mutations. Initial strategies for exome enrichment utilized a hybridization‐based capture approach. Recently, amplicon‐based methods were designed to simplify preparation and utilize smaller DNA inputs. We evaluated two hybridization capture‐based and two amplicon‐based whole‐exome sequencing approaches, utilizing both Illumina and Ion Torrent sequencers, comparing on‐target alignment, uniformity, and variant calling. While the amplicon methods had higher on‐target rates, the hybridization capture‐based approaches demonstrated better uniformity. All methods identified many of the same single‐nucleotide variants, but each amplicon‐based method missed variants detected by the other three methods and reported additional variants discordant with all three other technologies. Many of these potential false positives or negatives appear to result from limited coverage, low variant frequency, vicinity to read starts/ends, or the need for platform‐specific variant calling algorithms. All methods demonstrated effective copy‐number variant calling when evaluated against a single‐nucleotide polymorphism array. This study illustrates some differences between whole‐exome sequencing approaches, highlights the need for selecting appropriate variant calling based on capture method, and will aid laboratories in selecting their preferred approach. PMID:26110913

  5. Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing.

    Science.gov (United States)

    Samorodnitsky, Eric; Jewell, Benjamin M; Hagopian, Raffi; Miya, Jharna; Wing, Michele R; Lyon, Ezra; Damodaran, Senthilkumar; Bhatt, Darshna; Reeser, Julie W; Datta, Jharna; Roychowdhury, Sameek

    2015-09-01

    Next-generation sequencing has aided characterization of genomic variation. While whole-genome sequencing may capture all possible mutations, whole-exome sequencing remains cost-effective and captures most phenotype-altering mutations. Initial strategies for exome enrichment utilized a hybridization-based capture approach. Recently, amplicon-based methods were designed to simplify preparation and utilize smaller DNA inputs. We evaluated two hybridization capture-based and two amplicon-based whole-exome sequencing approaches, utilizing both Illumina and Ion Torrent sequencers, comparing on-target alignment, uniformity, and variant calling. While the amplicon methods had higher on-target rates, the hybridization capture-based approaches demonstrated better uniformity. All methods identified many of the same single-nucleotide variants, but each amplicon-based method missed variants detected by the other three methods and reported additional variants discordant with all three other technologies. Many of these potential false positives or negatives appear to result from limited coverage, low variant frequency, vicinity to read starts/ends, or the need for platform-specific variant calling algorithms. All methods demonstrated effective copy-number variant calling when evaluated against a single-nucleotide polymorphism array. This study illustrates some differences between whole-exome sequencing approaches, highlights the need for selecting appropriate variant calling based on capture method, and will aid laboratories in selecting their preferred approach. PMID:26110913

  6. MutS recognition: Multiple mismatches and sequence context effects

    Indian Academy of Sciences (India)

    Amita Joshi; Basuthkar J Rao

    2001-12-01

    Escherichia coli MutS is a versatile repair protein that specifically recognizes not only various types of mismatches but also single stranded loops of up to 4 nucleotides in length. Specific binding, followed by the next step of tracking the DNA helix that locates hemi-methylated sites, is regulated by the conformational state of the protein as a function of ATP binding/hydrolysis. Here, we study how various molecular determinants of a heteroduplex regulate mismatch recognition by MutS, the critical first step of mismatch repair. Using classical DNase I footprinting assays, we demonstrate that the hierarchy of MutS binding to various types of mismatches is identical whether the mismatches are present singly or in multiples. Moreover, this unique hierarchy is indifferent both to the differential level of DNA helical flexibility and to the unpaired status of the mismatched bases in a heteroduplex. Surprisingly, multiple mismatches exhibit reduced affinity of binding to MutS, compared to that of a similar single mismatch. Such a reduction in the affinity might be due to sequence context effects, which we established more directly by studying two identical single mismatches in an altered sequence background. A mismatch, upon simply being flipped at the same location, elicits changes in MutS specific contacts, thereby underscoring the importance of sequence context in modulating MutS binding to mismatches.

  7. Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences

    OpenAIRE

    Park Yungki

    2009-01-01

    Abstract Background Protein-protein interactions underlie many important biological processes. Computational prediction methods can nicely complement experimental approaches for identifying protein-protein interactions. Recently, a unique category of sequence-based prediction methods has been put forward - unique in the sense that it does not require homologous protein sequences. This enables it to be universally applicable to all protein sequences unlike many of previous sequence-based predi...

  8. Effect of repeated insertions of curved sequences in DNA plasmids: a light-scattering study

    Science.gov (United States)

    Beretta, Stefano; Chirico, Giuseppe; Baldini, Giancarlo; Kapp, U.; Badaracco, G.

    1993-06-01

    The effect of the insertion of different amounts (from 0 to 6) of the curved sequence AluI in pUC18m plasmid (2686 base pairs, bp) is studied by dynamic light scattering. This sequence is a highly repeated 113 base pairs long sequence from Artemia Franciscana shrimp. A 30% compaction of the plasmids containing 2 and 6 adjacent AluI sequences compared to pUC8 plasmid (2717 bp) is observed. Furthermore the behavior of the translational diffusion coefficient Dt versus the number of adjacent AluI insertion is not monotonic.

  9. Label-Free and Sensitive Fluorescent Detection of Sequence-Specific Single-Strand DNA Based on S1 Nuclease Cleavage Effects

    OpenAIRE

    Guan, Zheng; Liu, Jinchuan; Bai, Wenhui; Lv, Zhenzhen; Jiang, Xiaoling; Yang, Shuming; Chen, Ailiang; Lv, Guiyuan

    2014-01-01

    The ability to detect sequence-specific single-strand DNA (ssDNA) in complex, contaminant-ridden samples, using a fluorescent method directly without a DNA extraction and PCR step could simplify the detection of pathogens in the field and in the clinic. Here, we have demonstrated a simple label-free sensing strategy to detect ssDNA by employing its complementary ssDNA, S1 nuclease and nucleic acid fluorescent dyes. Upon clearing away redundant complementary ssDNA and possibly mismatched doubl...

  10. Irradiation hardening of Fe-9Cr-based alloys and ODS Eurofer: Effect of helium implantation and iron-ion irradiation at 300 °C including sequence effects

    Science.gov (United States)

    Heintze, C.; Bergner, F.; Hernández-Mayoral, M.; Kögler, R.; Müller, G.; Ulbricht, A.

    2016-03-01

    Single-beam, dual-beam and sequential iron- and/or helium-ion irradiations are widely accepted to emulate more application-relevant but hardly accessible irradiation conditions of generation-IV fission and fusion candidate materials for certain purposes such as material pre-selection, identification of basic mechanisms or model calibration. However, systematic investigations of sequence effects capable to critically question individual approaches are largely missing. In the present study, sequence effects of iron-ion irradiations at 300 °C up to 5 dpa and helium implantations up to 100 appm He are investigated by means of post-irradiation nanoindentation of an Fe9%Cr model alloy, ferritic/martensitic 9%Cr steels T91 and Eurofer97 and oxide dispersion strengthened (ODS) Eurofer. Different types of sequence effects, both synergistic and antagonistic, are identified and tentative interpretations are suggested. It is found that different accelerated irradiation approaches have a great impact on the mechanical hardening. This stresses the importance of experimental design in attempts to emulate in-reactor conditions.

  11. Repeat Sequences and Base Correlations in Human Y Chromosome Palindromes

    Institute of Scientific and Technical Information of China (English)

    Neng-zhi Jin; Zi-xian Liu; Yan-jiao Qi; Wen-yuan Qiu

    2009-01-01

    On the basis of information theory and statistical methods, we use mutual information, n-tuple entropy and conditional entropy, combined with biological characteristics, to analyze the long range correlation and short range correlation in human Y chromosome palindromes. The magnitude distribution of the long range correlation which can be reflected by the mutual information is P5>P5a>P5b (P5a and P5b are the sequences that replace solely Alu repeats and all interspersed repeats with random uncorrelated sequences in human Y chromosome palindrome 5, respectively); and the magnitude distribution of the short range correlation which can be reflected by the n-tuple entropy and the conditional entropy is P5>P5a>P5b>random uncorrelated sequence. In other words, when the Alu repeats and all interspersed repeats replace with random uncorrelated sequence, the long range and short range correlation decrease gradually. However, the random uncorrelated sequence has no correlation. This research indicates that more repeat sequences result in stronger correlation between bases in human Y chromosome. The analyses may be helpful to understand the special structures of human Y chromosome palindromes profoundly.

  12. Protein Function Prediction Based on Sequence and Structure Information

    KAUST Repository

    Smaili, Fatima Z.

    2016-05-25

    The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

  13. Which Microbial Communities Are Present? Sequence-Based Metagenomics

    Science.gov (United States)

    Caffrey, Sean M.

    The use of metagenomic methods that directly sequence environmental samples has revealed the extraordinary microbial diversity missed by traditional culture-based methodologies. Therefore, to develop a complete and representative model of an environment's microbial community and activities, metagenomic analysis is an essential tool.

  14. How effective is graphene nanopore geometry on DNA sequencing?

    CERN Document Server

    Satarifard, Vahid; Ejtehadi, Mohammad Reza

    2015-01-01

    In this paper we investigate the effects of graphene nanopore geometry on homopolymer ssDNA pulling process through nanopore using steered molecular dynamic (SMD) simulations. Different graphene nanopores are examined including axially symmetric and asymmetric monolayer graphene nanopores as well as five layer graphene polyhedral crystals (GPC). The pulling force profile, moving fashion of ssDNA, work done in irreversible DNA pulling and orientations of DNA bases near the nanopore are assessed. Simulation results demonstrate the strong effect of the pore shape as well as geometrical symmetry on free energy barrier, orientations and dynamic of DNA translocation through graphene nanopore. Our study proposes that the symmetric circular geometry of monolayer graphene nanopore with high pulling velocity can be used for DNA sequencing.

  15. 3D Motion Parameters Determination Based on Binocular Sequence Images

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Exactly capturing three dimensional (3D) motion information of an object is an essential and important task in computer vision, and is also one of the most difficult problems. In this paper, a binocular vision system and a method for determining 3D motion parameters of an object from binocular sequence images are introduced. The main steps include camera calibration, the matching of motion and stereo images, 3D feature point correspondences and resolving the motion parameters. Finally, the experimental results of acquiring the motion parameters of the objects with uniform velocity and acceleration in the straight line based on the real binocular sequence images by the mentioned method are presented.

  16. DNA sequence analysis with droplet-based microfluidics

    OpenAIRE

    Abate, Adam R.; Hung, Tony; Sperling, Ralph A.; Mary, Pascaline; Rotem, Assaf; Agresti, Jeremy J.; Weiner, Michael A.; Weitz, David A.

    2013-01-01

    Droplet-based microfluidic techniques can form and process micrometer scale droplets at thousands per second. Each droplet can house an individual biochemical reaction, allowing millions of reactions to be performed in minutes with small amounts of total reagent. This versatile approach has been used for engineering enzymes, quantifying concentrations of DNA in solution, and screening protein crystallization conditions. Here, we use it to read the sequences of DNA molecules with a FRET-based ...

  17. Spectroscopic investigation on the telomeric DNA base sequence repeat

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Telomeres are protein-DNA complexes at the terminals of linear chromosomes, which protect chromosomal integrity and maintain cellular replicative capacity.From single-cell organisms to advanced animals and plants,structures and functions of telomeres are both very conservative. In cells of human and vertebral animals, telomeric DNA base sequences all are (TTAGGG)n. In the present work, we have obtained absorption and fluorescence spectra measured from seven synthesized oligonucleotides to simulate the telomeric DNA system and calculated their relative fluorescence quantum yields on which not only telomeric DNA characteristics are predicted but also possibly the shortened telomeric sequences during cell division are imrelative fluorescence quantum yield and remarkable excitation energy innerconversion, which tallies with the telomeric sequence of (TTAGGG)n. This result shows that telomeric DNA has a strong non-radiative or innerconvertible capability.``

  18. DUK - A Fast and Efficient Kmer Based Sequence Matching Tool

    Energy Technology Data Exchange (ETDEWEB)

    Li, Mingkun; Copeland, Alex; Han, James

    2011-03-21

    A new tool, DUK, is developed to perform matching task. Matching is to find whether a query sequence partially or totally matches given reference sequences or not. Matching is similar to alignment. Indeed many traditional analysis tasks like contaminant removal use alignment tools. But for matching, there is no need to know which bases of a query sequence matches which position of a reference sequence, it only need know whether there exists a match or not. This subtle difference can make matching task much faster than alignment. DUK is accurate, versatile, fast, and has efficient memory usage. It uses Kmer hashing method to index reference sequences and Poisson model to calculate p-value. DUK is carefully implemented in C++ in object oriented design. The resulted classes can also be used to develop other tools quickly. DUK have been widely used in JGI for a wide range of applications such as contaminant removal, organelle genome separation, and assembly refinement. Many real applications and simulated dataset demonstrate its power.

  19. An Uncompressed Image Encryption Algorithm Based on DNA Sequences

    Directory of Open Access Journals (Sweden)

    Shima Ramesh Maniyath

    2011-07-01

    Full Text Available The rapid growth of the Internet and digitized content made image and video distribution simpler. Hence the need for image and video data protection is on the rise. In this paper, we propose a secure and computationally feasible image and video encryption/decryption algorithm based on DNA sequences. The main purpose of this algorithm is to reduce the big image encryption time. This algorithm is implemented by using the natural DNA sequences as main keys. The first part is the process of pixel scrambling. The original image is confused in the light of the scrambling sequence which is generated by the DNA sequence. The second part is the process of pixel replacement. The pixel gray values of the new image and the one of the three encryption templates generated by the other DNA sequence are XORed bit-by-bit in turn. The main scope of this paper is to propose an extension of this algorithm to videos and making it secure using modern Biological technology. A security analysis for the proposed system is performed and presented.

  20. Test Case Generation Based on Use case and Sequence Diagram

    Directory of Open Access Journals (Sweden)

    Santosh Kumar Swain

    2010-07-01

    Full Text Available We present a comprehensive test case generation technique from UML models. We use the features in UML 2.0 sequence diagram including conditions, iterations, asynchronous messages and concurrent components. In our approach, test cases are derived from analysis artifacts such as use cases, their corresponding sequence diagrams and constraints specified across all these artifacts. We construct Use case Dependency Graph (UDG from use case diagram and Concurrent Control Flow Graph (CCFG from corresponding sequence diagrams for test sequence generation. We focus testing on sequences of messages among objects of use case scenarios. Our testing strategy derives test cases using full predicate coverage criteria. Our proposed test case generation technique can be used for integration and system testing accommodating the object message and condition information associated with the use case scenarios. The test cases thus generated are suitable for detecting synchronization and dependency of use cases and messages, object interaction and operational faults. Finally, we have made an analysis and comparison of our approach with existing approaches, which are based on other coverage criterion through an example.

  1. Different Sequences of Feedback Types: Effectiveness, Attitudes, and Preferences

    Science.gov (United States)

    Wanchid, Raveewan

    2015-01-01

    The purposes of this research were to: 1) to compare the effects of different sequences of feedback types on the students' writing ability and their effect size; 2) to compare the effects of the levels of general English proficiency (high, moderate, and low) on the students' writing ability and their effect size; 3) to investigate the interaction…

  2. Wavelet Based Lossless DNA Sequence Compression for Faster Detection of Eukaryotic Protein Coding Regions

    Directory of Open Access Journals (Sweden)

    G. N. Dash

    2012-07-01

    Full Text Available Discrimination of protein coding regions called exons from noncoding regions called introns or junk DNA in eukaryotic cell is a computationally intensive task. But the dimension of the DNA string is huge; hence it requires large computation time. Further the DNA sequences are inherently random and have vast redundancy, hidden regularities, long repeats and complementary palindromes and therefore cannot be compressed efficiently. The objective of this study is to present an integrated signal processing algorithm that considerably reduces the computational load by compressing the DNA sequence effectively and aids the problem of searching for coding regions in DNA sequences. The presented algorithm is based on the Discrete Wavelet Transform (DWT, a very fast and effective method used for data compression and followed by comb filter for effective prediction of protein coding period-3 regions in DNA sequences. This algorithm is validated using standard dataset such as HMR195, Burset and Guigo and KEGG.

  3. Automating the Photogrammetric Bridging Based on MMS Image Sequence Processing

    Science.gov (United States)

    Silva, J. F. C.; Lemes Neto, M. C.; Blasechi, V.

    2014-11-01

    The photogrammetric bridging or traverse is a special bundle block adjustment (BBA) for connecting a sequence of stereo-pairs and of determining the exterior orientation parameters (EOP). An object point must be imaged in more than one stereo-pair. In each stereo-pair the distance ratio between an object and its corresponding image point varies significantly. We propose to automate the photogrammetric bridging based on a fully automatic extraction of homologous points in stereo-pairs and on an arbitrary Cartesian datum to refer the EOP and tie points. The technique uses SIFT algorithm and the keypoint matching is given by similarity descriptors of each keypoint based on the smallest distance. All the matched points are used as tie points. The technique was applied initially to two pairs. The block formed by four images was treated by BBA. The process follows up to the end of the sequence and it is semiautomatic because each block is processed independently and the transition from one block to the next depends on the operator. Besides four image blocks (two pairs), we experimented other arrangements with block sizes of six, eight, and up to twenty images (respectively, three, four, five and up to ten bases). After the whole image pairs sequence had sequentially been adjusted in each experiment, a simultaneous BBA was run so to estimate the EOP set of each image. The results for classical ("normal case") pairs were analyzed based on standard statistics regularly applied to phototriangulation, and they show figures to validate the process.

  4. Revision of Begomovirus taxonomy based on pairwise sequence comparisons

    KAUST Repository

    Brown, Judith K.

    2015-04-18

    Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

  5. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

    Directory of Open Access Journals (Sweden)

    Martin Mascher

    Full Text Available The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS, a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new

  6. A Correlational Encoder Decoder Architecture for Pivot Based Sequence Generation

    OpenAIRE

    SAHA, AMRITA; Khapra, Mitesh M.; Chandar, Sarath; Rajendran, Janarthanan; Cho, Kyunghyun

    2016-01-01

    Interlingua based Machine Translation (MT) aims to encode multiple languages into a common linguistic representation and then decode sentences in multiple target languages from this representation. In this work we explore this idea in the context of neural encoder decoder architectures, albeit on a smaller scale and without MT as the end goal. Specifically, we consider the case of three languages or modalities X, Z and Y wherein we are interested in generating sequences in Y starting from inf...

  7. Development in Rice Genome Research Based on Accurate Genome Sequence

    OpenAIRE

    2008-01-01

    Rice is one of the most important crops in the world. Although genetic improvement is a key technology for the acceleration of rice breeding, a lack of genome information had restricted efforts in molecular-based breeding until the completion of the high-quality rice genome sequence, which opened new opportunities for research in various areas of genomics. The syntenic relationship of the rice genome to other cereal genomes makes the rice genome invaluable for understanding how cereal genomes...

  8. A Refinement of Perfect Equilibria Based On Substitute Sequences

    OpenAIRE

    Aliprantis, C. D.; I. Topolyan

    2009-01-01

    We propose an equilibrium refinement of strict perfect equilibrium for the finite normal form games, which is not known in the literature. Okada came up with the idea of strict perfect equilibrium by strengthening the main definition of a perfect equilibrium, due to Selten [14]. We consider the alternative (and equivalent) definition of perfect equilibrium, based on the substitute sequences, as appeared in Selten [14]. We show that by strengthening and modifiyng this definition slightly, one ...

  9. Sequencing of oligonucleotide phosphorothioates based on solid-supported desulfurization.

    OpenAIRE

    Wyrzykiewicz, T K; Cole, D L

    1994-01-01

    We described a solid-supported desulfurization procedure allowing easy access to the sequence analysis of oligonucleotide phosphorothioates. The described method is based upon selective removal of the 2-cyanoethyl phosphate protecting groups, followed by iodine-promoted desulfurization of the resulting phosphorothioate diesters. Automatic oxidation of oligonucleotide phosphorothioates, anchored via an ester linkage to a standard solid support (LCAA/CPG), is combined with Maxam-Gilbert solid-s...

  10. Effects of Sequence on Transmission Properties of DNA Molecules

    Institute of Scientific and Technical Information of China (English)

    DONG Rui-Xin; YAN Xun-Ling; YANG Bing

    2008-01-01

    A double helix model of charge transport in DNA molecule is given and the transmission spectra of four DNA sequences are obtained. The calculated results show that the transmission characteristics of DNA are not only related to the longitudinal transport but also to the transverse transport of molecule. The periodic sequence with the same composition has stronger conduction ability. With the increasing of bases composition, the conductive ability reduces, but the weight of θ direction rises in charge transfer.

  11. Effect of Noise on DNA Sequencing via Transverse Electronic Transport

    OpenAIRE

    Krems, Matt; Zwolak, Michael; Pershin, Yuriy V.; Di Ventra, Massimiliano

    2009-01-01

    Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow for rapid DNA sequencing. However, fluctuations of the environment, such as ionic and DNA motion, introduce important scattering processes that may affect the viability of this approach to sequencing. To understand this issue, we have analyzed a simple mod...

  12. Triple helix structures: sequence dependence, flexibility and mismatch effects.

    Science.gov (United States)

    Sun, J S; Mergny, J L; Lavery, R; Montenay-Garestier, T; Hélène, C

    1991-12-01

    By means of molecular modelling, electrostatic interactions are shown to play an important role in the sequence-dependent structure of triple helices formed by a homopyrimidine oligonucleotide bound to a homopurine. homopyrimidine sequence on DNA. This is caused by the presence of positive charges due to the protonation of cytosines in the Hoogsteen-bonded strand, required in order to form C.GxC+ triplets. Energetic and conformational characteristics of triple helices with different sequences are analyzed and discussed. The effects of duplex mismatches on the triple helix stability are investigated via thermal dissociation using UV absorption. PMID:1815635

  13. Sequence-Dependent Effects on the Properties of Semiflexible Biopolymers

    OpenAIRE

    Zhou, Zicong; Joos, Bela

    2008-01-01

    Using path integral technique, we show exactly that for a semiflexible biopolymer in constant extension ensemble, no matter how long the polymer and how large the external force, the effects of short range correlations in the sequence-dependent spontaneous curvatures and torsions can be incorporated into a model with well-defined mean spontaneous curvature and torsion as well as a renormalized persistence length. Moreover, for a long biopolymer with large mean persistence length, the sequence...

  14. Effects of halogenated WNA derivatives on sequence dependency for expansion of recognition sequences in non-natural-type triplexes.

    Science.gov (United States)

    Taniguchi, Yosuke; Nakamura, Ayako; Senko, Yusuke; Nagatsugi, Fumi; Sasaki, Shigeki

    2006-03-01

    Triplex-forming oligonucleotides (TFOs) are sequence-specific DNA-binding agents, but their target duplexes are limited to homopurine/homopyrimidine sequences because of interruption of the pyrimidines bases in the purine region. This problem has not been fully solved despite a wide variety of studies. Recently, we have developed a bicyclic system as a novel scaffold for nucleoside analogues (WNA, W-shaped nucleoside analogues) and determined two useful compounds, WNA-betaT (2) and WNA-betaC (5), for highly stable and selective triplex formation at a TA and a CG interrupting site, respectively. However, subsequent investigations have shown that the triplex formation using WNA is dependent on the neighboring bases of the TFOs. In this study, we have synthesized new WNA derivatives having halogenated recognition bases or benzene rings and evaluated the effects of the modifications on the triplex stability as well as selectivity. It has been found that the WNA-betaT analogues holding 5-halogenated pyrimidine bases (WNA-beta(Br)U (3) and WNA-beta(F)U (4)) exhibit high CG-selectivity. On the other hand, the WNA-betaT derivatives having the bromo-substituted benzene ring (mBr-WNA-betaT (10) and oBr-WNA-betaT (11)) have shown high selectivity to a TA interrupting site with high stability in the sequences to which the original WNA-betaT do not bind. Thus, sequence-dependency has been overcome by the sequence-dependent use of WNA-betaT, mBr-WNA-betaT, and oBr-WNA-betaT. PMID:16497000

  15. Translating sanger-based routine DNA diagnostics into generic massive parallel ion semiconductor sequencing

    NARCIS (Netherlands)

    Diekstra, A.; Bosgoed, E.A.J.; Rikken, A.; Lier, B. van; Kamsteeg, E.J.; Tychon, M.W.J.; Derks, R.C.; Soest, R.A.; Mensenkamp, A.R.; Scheffer, H.; Neveling, K.; Nelen, M.R.

    2015-01-01

    BACKGROUND: Dideoxy-based chain termination sequencing developed by Sanger is the gold standard sequencing approach and allows clinical diagnostics of disorders with relatively low genetic heterogeneity. Recently, new next generation sequencing (NGS) technologies have found their way into diagnostic

  16. MOST: a modified MLST typing tool based on short read sequencing.

    Science.gov (United States)

    Tewolde, Rediat; Dallman, Timothy; Schaefer, Ulf; Sheppard, Carmen L; Ashton, Philip; Pichon, Bruno; Ellington, Matthew; Swift, Craig; Green, Jonathan; Underwood, Anthony

    2016-01-01

    Multilocus sequence typing (MLST) is an effective method to describe bacterial populations. Conventionally, MLST involves Polymerase Chain Reaction (PCR) amplification of housekeeping genes followed by Sanger DNA sequencing. Public Health England (PHE) is in the process of replacing the conventional MLST methodology with a method based on short read sequence data derived from Whole Genome Sequencing (WGS). This paper reports the comparison of the reliability of MLST results derived from WGS data, comparing mapping and assembly-based approaches to conventional methods using 323 bacterial genomes of diverse species. The sensitivity of the two WGS based methods were further investigated with 26 mixed and 29 low coverage genomic data sets from Salmonella enteridis and Streptococcus pneumoniae. Of the 323 samples, 92.9% (n = 300), 97.5% (n = 315) and 99.7% (n = 322) full MLST profiles were derived by the conventional method, assembly- and mapping-based approaches, respectively. The concordance between samples that were typed by conventional (92.9%) and both WGS methods was 100%. From the 55 mixed and low coverage genomes, 89.1% (n = 49) and 67.3% (n = 37) full MLST profiles were derived from the mapping and assembly based approaches, respectively. In conclusion, deriving MLST from WGS data is more sensitive than the conventional method. When comparing WGS based methods, the mapping based approach was the most sensitive. In addition, the mapping based approach described here derives quality metrics, which are difficult to determine quantitatively using conventional and WGS-assembly based approaches. PMID:27602279

  17. Entamoeba histolytica: observations on metabolism based on thegenome sequence

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Iain J.; Loftus, Brendan J.

    2005-07-01

    The sequencing of the genome of Entamoeba histolytica has allowed a reconstruction of its metabolic pathways, many of which are unusual for a eukaryote. Based on the genome sequence, it appears that amino acids may play a larger role than previously thought in energy metabolism, with roles in both ATP synthesis and NAD regeneration. Arginine decarboxylase may be involved in survival of E. histolytica during its passage through the stomach. The usual pyrimidine synthesis pathway is absent, but a partial pyrimidine degradation pathway could be part of a novel pyrimidine synthesis pathway. Ribonucleotide reductase was not found in the E. histolytica genome, but it was found in the close relatives Entamoeba invadens and Entamoeba moshkovskii, suggesting a recent loss from E. histolytica. The usual eukaryotic glucose transporters are not present, but members of a prokaryotic monosaccharide transporter family are present.

  18. Protection technique based on Delta-zero sequence voltages for generator stator ground fault

    Energy Technology Data Exchange (ETDEWEB)

    Tai, N.L.; Ai, Q. [Shanghai Jiao Tong University (China). Dept. of Power Electrical Engineering

    2004-09-01

    A mathematical model on a coil basis is used to study the characteristics of the zero sequence voltage of a generator The proposed technique for the stator groundfault detection simultaneously takes into account the fault contributed zero sequence fundamental voltage and the fault contributed third-harmonic voltage (Delta-zero sequence voltage). The effect of the start-up component based on the wavelet transform is also highlighted. As information both on the fault contributed zero sequence fundamental voltage and the third-harmonic voltage is used simultaneously, the scheme can obtain higher sensitivity. Results from the experiment and in the field show that the proposed technique can detect the ground fault with high sensitivity and reliability during all operating conditions. (author)

  19. Generalization of entropy based divergence measures for symbolic sequence analysis.

    Directory of Open Access Journals (Sweden)

    Miguel A Ré

    Full Text Available Entropy based measures have been frequently used in symbolic sequence analysis. A symmetrized and smoothed form of Kullback-Leibler divergence or relative entropy, the Jensen-Shannon divergence (JSD, is of particular interest because of its sharing properties with families of other divergence measures and its interpretability in different domains including statistical physics, information theory and mathematical statistics. The uniqueness and versatility of this measure arise because of a number of attributes including generalization to any number of probability distributions and association of weights to the distributions. Furthermore, its entropic formulation allows its generalization in different statistical frameworks, such as, non-extensive Tsallis statistics and higher order Markovian statistics. We revisit these generalizations and propose a new generalization of JSD in the integrated Tsallis and Markovian statistical framework. We show that this generalization can be interpreted in terms of mutual information. We also investigate the performance of different JSD generalizations in deconstructing chimeric DNA sequences assembled from bacterial genomes including that of E. coli, S. enterica typhi, Y. pestis and H. influenzae. Our results show that the JSD generalizations bring in more pronounced improvements when the sequences being compared are from phylogenetically proximal organisms, which are often difficult to distinguish because of their compositional similarity. While small but noticeable improvements were observed with the Tsallis statistical JSD generalization, relatively large improvements were observed with the Markovian generalization. In contrast, the proposed Tsallis-Markovian generalization yielded more pronounced improvements relative to the Tsallis and Markovian generalizations, specifically when the sequences being compared arose from phylogenetically proximal organisms.

  20. Analysis of Sequence Based Classifier Prediction for HIV Subtypes

    Directory of Open Access Journals (Sweden)

    S. Santhosh Kumar

    2012-10-01

    Full Text Available Human immunodeficiency virus (HIV is a lent virus that causes acquired immunodeficiency syndrome (AIDS. The main drawback in HIV treatment process is its sub type prediction. The sub type and group classification of HIV is based on its genetic variability and location. HIV can be divided into two major types, HIV type 1 (HIV-1 and HIV type 2 (HIV-2. Many classifier approaches have been used to classify HIV subtypes based on their group, but some of cases are having two groups in one; in such cases the classification becomes more complex. The methodology used is this paper based on the HIV sequences. For this work several classifier approaches are used to classify the HIV1 and HIV2. For implementation of the work a real time patient database is taken and the patient records are experimented and the final best classifier is identified with quick response time and least error rate.

  1. Next-Generation Sequencing-Based Molecular Diagnosis of Choroideremia

    Directory of Open Access Journals (Sweden)

    Kayo Shimizu

    2015-07-01

    Full Text Available We screened patients with choroideremia using next-generation sequencing (NGS and identified a novel mutation and a known mutation in the CHM gene. One patient presented an atypical fundus appearance for choroideremia. Another patient presented macular hole retinal detachment in the left eye. The present case series shows the utility of NGS-based screening in patients with choroideremia. In addition, the presence of macular hole in 1 of the 2 patients, together with a previous report, indicated the susceptibility of patients with choroideremia to macular hole.

  2. The heterogeneous world of congruency sequence effects: an update.

    Science.gov (United States)

    Duthoo, Wout; Abrahamse, Elger L; Braem, Senne; Boehler, Carsten N; Notebaert, Wim

    2014-01-01

    Congruency sequence effects (CSEs) refer to the observation that congruency effects in conflict tasks are typically smaller following incongruent compared to following congruent trials. This measure has long been thought to provide a unique window into top-down attentional adjustments and their underlying brain mechanisms. According to the renowned conflict monitoring theory, CSEs reflect enhanced selective attention following conflict detection. Still, alternative accounts suggested that bottom-up associative learning suffices to explain the pattern of reaction times and error rates. A couple of years ago, a review by Egner (2007) pitted these two rivalry accounts against each other, concluding that both conflict adaptation and feature integration contribute to the CSE. Since then, a wealth of studies has further debated this issue, and two additional accounts have been proposed, offering intriguing alternative explanations. Contingency learning accounts put forward that predictive relationships between stimuli and responses drive the CSE, whereas the repetition expectancy hypothesis suggests that top-down, expectancy-driven control adjustments affect the CSE. In the present paper, we build further on the previous review (Egner, 2007) by summarizing and integrating recent behavioral and neurophysiological studies on the CSE. In doing so, we evaluate the relative contribution and theoretical value of the different attentional and memory-based accounts. Moreover, we review how all of these influences can be experimentally isolated, and discuss designs and procedures that can critically judge between them. PMID:25250005

  3. The heterogeneous world of congruency sequence effects: An update.

    Directory of Open Access Journals (Sweden)

    WoutDuthoo

    2014-09-01

    Full Text Available Congruency sequence effects (CSEs refer to the observation that congruency effects in conflict tasks are typically smaller following incongruent compared to following congruent trials. This measure has long been thought to provide a unique window into top-down attentional adjustments and their underlying brain mechanisms. According to the renowned conflict monitoring theory, CSEs reflect enhanced selective attention following conflict detection. Still, alternative accounts suggested that bottom-up associative learning suffices to explain the pattern of reaction times and error rates. A couple of years ago, a review by Egner (2007 pitted these two rivalry accounts against each other, concluding that both conflict adaptation and feature integration contribute to the CSE. Since then, a wealth of studies has further debated this issue, and two additional accounts have been proposed, offering intriguing alternative explanations. Contingency learning accounts put forward that predictive relationships between stimuli and responses drive the CSE, whereas the repetition expectancy hypothesis suggests that top-down, expectancy-driven control adjustments affect the CSE. In the present paper, we build further on the previous review (Egner, 2007 by summarizing and integrating recent behavioural and neurophysiological studies on the CSE. In doing so, we evaluate the relative contribution and theoretical value of the different attentional and memory-based accounts. Moreover, we review how all of these influences can be experimentally isolated, and discuss designs and procedures that can critically judge between them.

  4. Study design requirements for RNA sequencing-based breast cancer diagnostics.

    Science.gov (United States)

    Mer, Arvind Singh; Klevebring, Daniel; Grönberg, Henrik; Rantalainen, Mattias

    2016-01-01

    Sequencing-based molecular characterization of tumors provides information required for individualized cancer treatment. There are well-defined molecular subtypes of breast cancer that provide improved prognostication compared to routine biomarkers. However, molecular subtyping is not yet implemented in routine breast cancer care. Clinical translation is dependent on subtype prediction models providing high sensitivity and specificity. In this study we evaluate sample size and RNA-sequencing read requirements for breast cancer subtyping to facilitate rational design of translational studies. We applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models (unsupervised and supervised). Subtype classification accuracy improved with increasing sample size up to N = 750 (accuracy = 0.93), although with a modest improvement beyond N = 350 (accuracy = 0.92). Prediction of routine biomarkers achieved accuracy of 0.94 (ER) and 0.92 (Her2) at N = 200. Subtype classification improved with RNA-sequencing library size up to 5 million reads. Development of molecular subtyping models for cancer diagnostics requires well-designed studies. Sample size and the number of RNA sequencing reads directly influence accuracy of molecular subtyping. Results in this study provide key information for rational design of translational studies aiming to bring sequencing-based diagnostics to the clinic. PMID:26830453

  5. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

    Science.gov (United States)

    Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylat...

  6. Implications of HLA sequence-based typing in transplantation

    Directory of Open Access Journals (Sweden)

    Shankarkumar U

    2008-01-01

    Full Text Available Serology-based conventional microlymphocytotoxicity HLA typing method, which has been regarded as the gold standard in organ and hematopoietic stem cell transplantation, has been replaced now by DNA-based typing. Many laboratories all over the world have already switched over to molecular methods. Microlymphocytotoxicity-based tissue typing was done using commercial sera, while the molecular typing by genomic DNA based. DNA quality and its quantity obtained using various DNA extraction protocols was found to be an important factor in the molecular method of tissue typing in transplant outcome. Many polymerase chain reaction-based molecular techniques have been adopted with far reaching clinical outcome. The sequence-based typing (SBT has been the ultimate technique, which has been of the highest reliability in defining the HLA alleles. The nonavailability of specific HLA antisera from native populations, large number of blank alleles yet to be defined and comparable low resolution of HLA alleles in SSP or SSOP technique, suggests that highly refined DNA-based methods like SBT should be used as an adjunct to HLA serology and/or low/intermediate/high resolution HLA typing in order to achieve a better transplant outcome.

  7. Security Analysis of a Block Encryption Algorithm Based on Dynamic Sequences of Multiple Chaotic Systems

    Institute of Scientific and Technical Information of China (English)

    DU Mao-Kang; HE Bo; WANG Yong

    2011-01-01

    Recently, the cryptosystem based on chaos has attracted much attention. Wang and Yu (Commun. Nonlin. Sci. Numer. Simulat. 14(2009)574) proposed a block encryption algorithm based on dynamic sequences of multiple chaotic systems. We analyze the potential Saws in the algorithm. Then, a chosen-plaintext attack is presented. Some remedial measures are suggested to avoid the flaws effectively. Furthermore, an improved encryption algorithm is proposed to resist the attacks and to keep all the merits of the original cryptosystem.

  8. The Sequence Effect in Parkinson’s Disease

    Directory of Open Access Journals (Sweden)

    Suk Yun Kang

    2011-05-01

    Full Text Available Background and Purpose The sequence effect (SE in Parkinson’s disease (PD denotes progressive slowness in speed or progressive decrease in amplitude of repetitive movements. It is a well-known feature of bradykinesia and is considered unique in PD. Until now, it was well-documented in advanced PD, but not in drug-naïve PD. The aim of this study is to know whether the SE can also be measured in drug-naïve PD. Methods We measured the SE with a computer-based, modified Purdue pegboard in 4 drug-naïve PD patients, which matched our previous study with advanced PD patients. Results We observed progressive slowness during movement, that is, SE. Statistical analysis showed a strong statistical trend toward the SE with the right hand, but no significance with the left hand. There was no statistical significance of SE with either the more or less affected hands. Conclusions These results indicate that the SE can be identified in drug-naïve PD, as well as in advanced PD, with objective measurements and support the idea that the SE is a feature in PD observed during the early stage of the disease without medication.

  9. Development of Sequence-Based Microsatellite Marker for Phalaenopsis Orchid

    Directory of Open Access Journals (Sweden)

    FATIMAH

    2011-06-01

    Full Text Available Phalaenopsis is one of the most interesting genera of orchids due to the members are often used as parents to produce hybrids. The establishment and development of highly reliable and discriminatory methods for identifying species and cultivars has become increasingly more important to plant breeders and members of the nursery industry. The aim of this research was to develop sequence-based microsatellite (eSSR markers for the Phalaenopsis orchid designed from the sequence of GenBank NCBI. Seventeen primers were designed and thirteen primers pairs could amplify the DNA giving the expected PCR product with polymorphism. A total of 51 alleles, with an average of 3 alleles per locus and polymorphism information content (PIC values at 0.674, were detected at the 16 SSR loci. Therefore, these markers could be used for identification of the Phalaenopsis orchid used in this study. Genetic similarity and principle coordinate analysis identified five major groups of Phalaenopsis sp. the first group consisted of P. amabilis, P. fuscata, P. javanica, and P. zebrine. The second group consisted of P. amabilis, P. amboinensis, P. bellina, P. floresens, and P. mannii. The third group consisted of P. bellina, P. cornucervi, P. cornucervi, P. violaceae sumatra, P. modesta. The forth group consisted of P. cornucervi and P. lueddemanniana, and the fifth group was P. amboinensis.

  10. Will my protein crystallize? A sequence-based predictor.

    Science.gov (United States)

    Smialowski, Pawel; Schmidt, Thorsten; Cox, Jürgen; Kirschner, Andreas; Frishman, Dmitrij

    2006-02-01

    We propose a machine-learning approach to sequence-based prediction of protein crystallizability in which we exploit subtle differences between proteins whose structures were solved by X-ray analysis [or by both X-ray and nuclear magnetic resonance (NMR) spectroscopy] and those proteins whose structures were solved by NMR spectroscopy alone. Because the NMR technique is usually applied on relatively small proteins, sequence length distributions of the X-ray and NMR datasets were adjusted to avoid predictions biased by protein size. As feature space for classification, we used frequencies of mono-, di-, and tripeptides represented by the original 20-letter amino acid alphabet as well as by several reduced alphabets in which amino acids were grouped by their physicochemical and structural properties. The classification algorithm was constructed as a two-layered structure in which the output of primary support vector machine classifiers operating on peptide frequencies was combined by a second-level Naive Bayes classifier. Due to the application of metamethods for cost sensitivity, our method is able to handle real datasets with unbalanced class representation. An overall prediction accuracy of 67% [65% on the positive (crystallizable) and 69% on the negative (noncrystallizable) class] was achieved in a 10-fold cross-validation experiment, indicating that the proposed algorithm may be a valuable tool for more efficient target selection in structural genomics. A Web server for protein crystallizability prediction called SECRET is available at http://webclu.bio.wzw.tum.de:8080/secret. PMID:16315316

  11. Similarity Measurement of Web Sessions Based on Sequence Alignment

    Institute of Scientific and Technical Information of China (English)

    LI Chaofeng; LU Yansheng

    2007-01-01

    The task of clustering Web sessions is to group Web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-group similarity.The first and foremost question needed to be considered in clustering Web sessions is how to measure the similarity between Web sessions. However, there are many shortcomings in traditional measurements. This paper introduces a new method for measuring similarities between Web pages that takes into account not only the URL but also the viewing time of the visited Web page. Then we give a new method to measure the similarity of Web sessions using sequence alignment and the similarity of Web page access in detail.Experiments have proved that our method is valid and efficient.

  12. An Effective Identification of Species from DNA Sequence: A Classification Technique by Integrating DM and ANN

    Directory of Open Access Journals (Sweden)

    Sathish Kumar S

    2012-08-01

    Full Text Available Species classification from DNA sequences remains as an open challenge in the area of bioinformatics, which deals with the collection, processing and analysis of DNA and proteomic sequence. Though incorporation of data mining can guide the process to perform well, poor definition, and heterogeneous nature of gene sequence remains as a barrier. In this paper, an effective classification technique to identify the organism from its gene sequence is proposed. The proposed integrated technique is mainly based on pattern mining and neural network-based classification. In pattern mining, the technique mines nucleotide patterns and their support from selected DNA sequence. The high dimension of the mined dataset is reduced using Multilinear Principal Component Analysis (MPCA. In classification, a well-trained neural network classifies the selected gene sequence and so the organism is identified even from a part of the sequence. The proposed technique is evaluated by performing 10-fold cross validation, a statistical validation measure, and the obtained results prove the efficacy of the technique.

  13. Simultaneous genomic identification and profiling of a single cell using semiconductor-based next generation sequencing

    Directory of Open Access Journals (Sweden)

    Manabu Watanabe

    2014-09-01

    Full Text Available Combining single-cell methods and next-generation sequencing should provide a powerful means to understand single-cell biology and obviate the effects of sample heterogeneity. Here we report a single-cell identification method and seamless cancer gene profiling using semiconductor-based massively parallel sequencing. A549 cells (adenocarcinomic human alveolar basal epithelial cell line were used as a model. Single-cell capture was performed using laser capture microdissection (LCM with an Arcturus® XT system, and a captured single cell and a bulk population of A549 cells (≈106 cells were subjected to whole genome amplification (WGA. For cell identification, a multiplex PCR method (AmpliSeq™ SNP HID panel was used to enrich 136 highly discriminatory SNPs with a genotype concordance probability of 1031–35. For cancer gene profiling, we used mutation profiling that was performed in parallel using a hotspot panel for 50 cancer-related genes. Sequencing was performed using a semiconductor-based bench top sequencer. The distribution of sequence reads for both HID and Cancer panel amplicons was consistent across these samples. For the bulk population of cells, the percentages of sequence covered at coverage of more than 100× were 99.04% for the HID panel and 98.83% for the Cancer panel, while for the single cell percentages of sequence covered at coverage of more than 100× were 55.93% for the HID panel and 65.96% for the Cancer panel. Partial amplification failure or randomly distributed non-amplified regions across samples from single cells during the WGA procedures or random allele drop out probably caused these differences. However, comparative analyses showed that this method successfully discriminated a single A549 cancer cell from a bulk population of A549 cells. Thus, our approach provides a powerful means to overcome tumor sample heterogeneity when searching for somatic mutations.

  14. GPCODON ALIGNMENT: A GLOBAL PAIRWISE CODON BASED SEQUENCE ALIGNMENT APPROACH

    Directory of Open Access Journals (Sweden)

    Zeinab A. Fareed

    2016-02-01

    Full Text Available The alignment of two DNA sequences is a basic step in the analysis of biological data. Sequencing a long DNA sequence is one of the most interesting problems in bioinformatics. Several techniques have been developed to solve this sequence alignment problem like dynamic programming and heuristic algorithms. In this paper, we introduce (GPCodon alignment a pairwise DNA-DNA method for global sequence alignment that improves the accuracy of pairwise sequence alignment. We use a new scoring matrix to produce the final alignment called the empirical codon substitution matrix. Using this matrix in our technique enabled the discovery of new relationships between sequences that could not be discovered using traditional matrices. In addition, we present experimental results that show the performance of the proposed technique over eleven datasets of average length of 2967 bps. We compared the efficiency and accuracy of our techniques against a comparable tool called “Pairwise Align Codons” [1].

  15. A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

    OpenAIRE

    Fei Chen; Yuan-Ting Zhang

    2003-01-01

    DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT) – the bionic wavelet transform (BWT) – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the s...

  16. SIMILARITY ANALYSIS OF DNA SEQUENCES BASED ON THE CHEMICAL PROPERTIES OF NUCLEOTIDE BASES, FREQUENCY AND POSITION OF GROUP MUTATIONS

    Directory of Open Access Journals (Sweden)

    Fatima KABLI

    2016-01-01

    Full Text Available The DNA sequences similarity analysis approaches have been based on the representation and the frequency of sequences components; however, the position inside sequence is important information for the sequence data. Whereas, insufficient information in sequences representations is important reason that causes poor similarity results. Based on three classifications of the DNA bases according to their chemical properties, the frequencies and average positions of group mutations have been grouped into two twelve-components vectors, the Euclidean distances among introduced vectors applied to compare the coding sequences of the first exon of beta globin gene of 11 species.

  17. Capturing Human Motion based on Modified Hidden Markov Model in Multi-View Image Sequences

    OpenAIRE

    Yanan Liu; Lian Kun Jia; Wen Yu Yu

    2014-01-01

    Human motion capturing is of great importance in video information retrieval, hence, in this paper, we propose a novel approach to effectively capturing human motions based on modified hidden markov model from multi-view image sequences. Firstly, the structure of the human skeleton model is illustrated, which is extended from skeleton root and spine root, and this skeleton consists of right leg, left leg and spine. Secondly, our proposed human motion capturing system is made up of data traini...

  18. PCR-based assays versus direct sequencing for evaluating the effect of KRAS status on anti-EGFR treatment response in colorectal cancer patients: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Lianfeng Shan

    Full Text Available BACKGROUND: The survival rate of colorectal cancer (CRC patients carrying wild-type KRAS is significantly increased by combining anti-EGFR monoclonal antibody (mAb with standard chemotherapy. However, conflicting data exist in both the wild-type KRAS and mutant KRAS groups, which strongly challenge CRC anti-EGFR treatment. Here we conducted a meta-analysis in an effort to provide more reliable information regarding anti-EGFR treatment in CRC patients. METHODS: We searched full reports of randomized clinical trials using Medline, the American Society of Clinical Oncology (ASCO, and the European Society for Medical Oncology (ESMO. Two investigators independently screened the published literature according to our inclusive and exclusive criteria and the relative data were extracted. We used Review Manager 5.2 software to analyze the data. RESULTS: The addition of anti-EGFR mAb to standard chemotherapy significantly improved both progression-free survival (PFS and median overall survival (mOS in the wild-type KRAS group; hazard ratios (HRs for PFS and mOS were 0.70 [95% confidence interval (CI, 0.58-0.84] and 0.83 [95% CI, 0.75-0.91], respectively. In sub-analyses of the wild-type KRAS group, when PCR-based assays are employed, PFS and mOS notably increase: the HRs were 0.74 [95% CI, 0.62-0.88] and 0.87 [95% CI, 0.78-0.96], respectively. In sub-analyses of the mutant KRAS group, neither PCR-based assays nor direct sequencing enhance PFS or mOS. CONCLUSION: Our data suggest that PCR-based assays with high sensitivity and specificity allow accurate identification of patients with wild-type KRAS and thus increase PFS and mOS. Furthermore, such assays liberate patients with mutant KRAS from unnecessary drug side effects, and provide them an opportunity to receive appropriate treatment. Thus, establishing a precise standard reference test will substantially optimize CRC-targeted therapies.

  19. Java Implementation based Heterogeneous Video Sequence Automated Surveillance Monitoring

    Directory of Open Access Journals (Sweden)

    Sankari Muthukarupan

    2013-04-01

    Full Text Available Automated video based surveillance monitoring is an essential and computationally challenging task to resolve issues in the secure access localities. This paper deals with some of the issues which are encountered in the integration surveillance monitoring in the real-life circumstances. We have employed video frames which are extorted from heterogeneous video formats. Each video frame is chosen to identify the anomalous events which are occurred in the sequence of time-driven process. Background subtraction is essentially required based on the optimal threshold and reference frame. Rest of the frames are ablated from reference image, hence all the foreground images paradigms are obtained. The co-ordinate existing in the deducted images is found by scanning the images horizontally until the occurrence of first black pixel. Obtained coordinate is twinned with existing co-ordinates in the primary images. The twinned co-ordinate in the primary image is considered as an active-region-of-interest. At the end, the starred images are converted to temporal video that scrutinizes the moving silhouettes of human behaviors in a static background. The proposed model is implemented in Java. Results and performance analysis are carried out in the real-life environments.

  20. Autonomously Generating Operations Sequences for a Mars Rover Using Artificial Intelligence-Based Planning

    Science.gov (United States)

    Sherwood, R.; Mutz, D.; Estlin, T.; Chien, S.; Backes, P.; Norris, J.; Tran, D.; Cooper, B.; Rabideau, G.; Mishkin, A.; Maxwell, S.

    2001-07-01

    This article discusses a proof-of-concept prototype for ground-based automatic generation of validated rover command sequences from high-level science and engineering activities. This prototype is based on ASPEN, the Automated Scheduling and Planning Environment. This artificial intelligence (AI)-based planning and scheduling system will automatically generate a command sequence that will execute within resource constraints and satisfy flight rules. An automated planning and scheduling system encodes rover design knowledge and uses search and reasoning techniques to automatically generate low-level command sequences while respecting rover operability constraints, science and engineering preferences, environmental predictions, and also adhering to hard temporal constraints. This prototype planning system has been field-tested using the Rocky 7 rover at JPL and will be field-tested on more complex rovers to prove its effectiveness before transferring the technology to flight operations for an upcoming NASA mission. Enabling goal-driven commanding of planetary rovers greatly reduces the requirements for highly skilled rover engineering personnel. This in turn greatly reduces mission operations costs. In addition, goal-driven commanding permits a faster response to changes in rover state (e.g., faults) or science discoveries by removing the time-consuming manual sequence validation process, allowing rapid "what-if" analyses, and thus reducing overall cycle times.

  1. Effective automated feature construction and selection for classification of biological sequences.

    Directory of Open Access Journals (Sweden)

    Uday Kamath

    Full Text Available Many open problems in bioinformatics involve elucidating underlying functional signals in biological sequences. DNA sequences, in particular, are characterized by rich architectures in which functional signals are increasingly found to combine local and distal interactions at the nucleotide level. Problems of interest include detection of regulatory regions, splice sites, exons, hypersensitive sites, and more. These problems naturally lend themselves to formulation as classification problems in machine learning. When classification is based on features extracted from the sequences under investigation, success is critically dependent on the chosen set of features.We present an algorithmic framework (EFFECT for automated detection of functional signals in biological sequences. We focus here on classification problems involving DNA sequences which state-of-the-art work in machine learning shows to be challenging and involve complex combinations of local and distal features. EFFECT uses a two-stage process to first construct a set of candidate sequence-based features and then select a most effective subset for the classification task at hand. Both stages make heavy use of evolutionary algorithms to efficiently guide the search towards informative features capable of discriminating between sequences that contain a particular functional signal and those that do not.To demonstrate its generality, EFFECT is applied to three separate problems of importance in DNA research: the recognition of hypersensitive sites, splice sites, and ALU sites. Comparisons with state-of-the-art algorithms show that the framework is both general and powerful. In addition, a detailed analysis of the constructed features shows that they contain valuable biological information about DNA architecture, allowing biologists and other researchers to directly inspect the features and potentially use the insights obtained to assist wet-laboratory studies on retainment or modification

  2. CLUSS: Clustering of protein sequences based on a new similarity measure

    Directory of Open Access Journals (Sweden)

    Brzezinski Ryszard

    2007-08-01

    Full Text Available Abstract Background The rapid burgeoning of available protein data makes the use of clustering within families of proteins increasingly important. The challenge is to identify subfamilies of evolutionarily related sequences. This identification reveals phylogenetic relationships, which provide prior knowledge to help researchers understand biological phenomena. A good evolutionary model is essential to achieve a clustering that reflects the biological reality, and an accurate estimate of protein sequence similarity is crucial to the building of such a model. Most existing algorithms estimate this similarity using techniques that are not necessarily biologically plausible, especially for hard-to-align sequences such as proteins with different domain structures, which cause many difficulties for the alignment-dependent algorithms. In this paper, we propose a novel similarity measure based on matching amino acid subsequences. This measure, named SMS for Substitution Matching Similarity, is especially designed for application to non-aligned protein sequences. It allows us to develop a new alignment-free algorithm, named CLUSS, for clustering protein families. To the best of our knowledge, this is the first alignment-free algorithm for clustering protein sequences. Unlike other clustering algorithms, CLUSS is effective on both alignable and non-alignable protein families. In the rest of the paper, we use the term "phylogenetic" in the sense of "relatedness of biological functions". Results To show the effectiveness of CLUSS, we performed an extensive clustering on COG database. To demonstrate its ability to deal with hard-to-align sequences, we tested it on the GH2 family. In addition, we carried out experimental comparisons of CLUSS with a variety of mainstream algorithms. These comparisons were made on hard-to-align and easy-to-align protein sequences. The results of these experiments show the superiority of CLUSS in yielding clusters of proteins

  3. Effects of interlinker sequences on the biological properties of bispecific single-chain antibodies

    Institute of Scientific and Technical Information of China (English)

    FANG Min; JIANG Xin; YANG Zhi; YIN Changcheng; LI Hua; ZHAO Rui; ZHANG Zhong; LIN Qing; HUANG Hualiang

    2003-01-01

    Single-chain bispecific antibody (scBsAb) is one of the promising genetic engineering antibody formats for clinical application. But the effects of interlinker sequences on the biological properties of bispecific single-chain antibodies have not been studied in detail. Three interlinker sequences were designed and synthesized, and denominated as Fc, HSA, 205C′, respectively. Universal vectors with these different interlinker sequences for scBsAb expression in E. coli were constructed. A model scBsAb based on a reshaped single-chain antibody (scFv) against human CD3 and a scFv directed against human ovarian carcinoma were generated and expressed in E. coli. The results of SDS-PAGE and Western blot showed that the different interlinker sequences did not affect the expression levelof scBsAb. However, as demonstrated by ELISA and pharmacokinetics studies performed in mice, scBsAbs with different interlinker sequences had difference in the antigen-binding activities and terminal half-life time (T1/2β) in vivo, the interlinker HSA could remarkably prolong the retention time of scBsAb in blood. These results indicated that the peptide sequence of interlinker could affect important biological properties of scBsAb, such as antigen-binding properties and stability in vivo. So, selection of an appropriate interlinker sequence is very important for scBsAb construction. Optimal interlinker can bring scBsAb biologicalproperties more suitable for clinical application.

  4. Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine.

    Science.gov (United States)

    Green, Robert C; Goddard, Katrina A B; Jarvik, Gail P; Amendola, Laura M; Appelbaum, Paul S; Berg, Jonathan S; Bernhardt, Barbara A; Biesecker, Leslie G; Biswas, Sawona; Blout, Carrie L; Bowling, Kevin M; Brothers, Kyle B; Burke, Wylie; Caga-Anan, Charlisse F; Chinnaiyan, Arul M; Chung, Wendy K; Clayton, Ellen W; Cooper, Gregory M; East, Kelly; Evans, James P; Fullerton, Stephanie M; Garraway, Levi A; Garrett, Jeremy R; Gray, Stacy W; Henderson, Gail E; Hindorff, Lucia A; Holm, Ingrid A; Lewis, Michelle Huckaby; Hutter, Carolyn M; Janne, Pasi A; Joffe, Steven; Kaufman, David; Knoppers, Bartha M; Koenig, Barbara A; Krantz, Ian D; Manolio, Teri A; McCullough, Laurence; McEwen, Jean; McGuire, Amy; Muzny, Donna; Myers, Richard M; Nickerson, Deborah A; Ou, Jeffrey; Parsons, Donald W; Petersen, Gloria M; Plon, Sharon E; Rehm, Heidi L; Roberts, J Scott; Robinson, Dan; Salama, Joseph S; Scollon, Sarah; Sharp, Richard R; Shirts, Brian; Spinner, Nancy B; Tabor, Holly K; Tarczy-Hornoch, Peter; Veenstra, David L; Wagle, Nikhil; Weck, Karen; Wilfond, Benjamin S; Wilhelmsen, Kirk; Wolf, Susan M; Wynn, Julia; Yu, Joon-Ho

    2016-06-01

    Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine. PMID:27181682

  5. Complete chloroplast genome sequence of Fritillaria unibracteata var. wabuensis based on SMRT Sequencing Technology.

    Science.gov (United States)

    Li, Ying; Li, Qiushi; Li, Xiwen; Song, Jingyuan; Sun, Chao

    2016-09-01

    Fritillaria unibracteata var. wabuensis is an important medicinal plant used for the treatment of cough symptoms related to the respiratory system. The chloroplast genome of F. unibracteata var. wabuensis (GenBank accession no. KF769142) was assembled using the PacBio RS platform (Pacific Biosciences, Beverly, MA) as a circle sequence with 151 009 bp. The assembled genome contains 133 genes, including 88 protein-coding, 37 tRNA, and eight rRNA genes. This genome sequence will provide important resource for further studies on the evolution of Fritillaria genus and molecular identification of Fritillaria herbs and their adulterants. This work suggests that PacBio RS is a powerful tool to sequence and assemble chloroplast genomes. PMID:26370383

  6. Sequence-Dependent Effects on the Properties of Semiflexible Biopolymers

    CERN Document Server

    Zicong, Bela

    2008-01-01

    Using path integral technique, we show exactly that for a semiflexible biopolymer in constant extension ensemble, no matter how long the polymer and how large the external force, the effects of short range correlations in the sequence-dependent spontaneous curvatures and torsions can be incorporated into a model with well-defined mean spontaneous curvature and torsion as well as a renormalized persistence length. Moreover, for a long biopolymer with large mean persistence length, the sequence-dependent persistence lengths can be replaced by their mean. However, for a short biopolymer or for a biopolymer with small persistence lengths, inhomogeneity in persistence lengths tends to make physical observables very sensitive to details and therefore less predictable.

  7. Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality.

    Science.gov (United States)

    Churchill, Jennifer D; King, Jonathan L; Chakraborty, Ranajit; Budowle, Bruce

    2016-09-01

    Massively parallel sequencing (MPS) offers substantial improvements over current forensic DNA typing methodologies such as increased resolution, scalability, and throughput. The Ion PGM™ is a promising MPS platform for analysis of forensic biological evidence. The system employs a sequencing-by-synthesis chemistry on a semiconductor chip that measures a pH change due to the release of hydrogen ions as nucleotides are incorporated into the growing DNA strands. However, implementation of MPS into forensic laboratories requires a robust chemistry. Ion Torrent's Hi-Q™ Sequencing Chemistry was evaluated to determine if it could improve on the quality of the generated sequence data in association with selected genetic marker targets. The whole mitochondrial genome and the HID-Ion STR 10-plex panel were sequenced on the Ion PGM™ system with the Ion PGM™ Sequencing 400 Kit and the Ion PGM™ Hi-Q™ Sequencing Kit. Concordance, coverage, strand balance, noise, and deletion ratios were assessed in evaluating the performance of the Ion PGM™ Hi-Q™ Sequencing Kit. The results indicate that reliable, accurate data are generated and that sequencing through homopolymeric regions can be improved with the use of Ion Torrent's Hi-Q™ Sequencing Chemistry. Overall, the quality of the generated sequencing data supports the potential for use of the Ion PGM™ in forensic genetic laboratories. PMID:27025714

  8. Effects of priming goal pursuit on implicit sequence learning

    Science.gov (United States)

    Gamble, Katherine R.; Lee, Joanna M.; Howard, James H.; Howard, Darlene V.

    2016-01-01

    Implicit learning, the type of learning that occurs without intent to learn or awareness of what has been learned, has been thought to be insensitive to the effects of priming, but recent studies suggest this is not the case. One study found that learning in the Serial Reaction Time (SRT) task was improved by nonconscious goal pursuit, primed via a word search task (Eitam et al., 2008). In two studies, we used the goal priming word search task from Eitam et al., but with a different version of the SRT, the Alternating Serial Reaction Time task (ASRT). Unlike the SRT, which often results in explicit knowledge and assesses sequence learning at one point in time, the ASRT has been shown to be implicit through sensitive measures of judgment, and it enables sequence learning to be measured continuously. In both studies, we found that implicit learning was superior in the groups that were primed for goal achievement compared to control groups, but the effect was transient. We discuss possible reasons for the observed time course of the positive effects of goal priming, as well as some future areas of investigation to better understand the mechanisms that underlie this effect, which could lead to methods to prolong the positive effects. PMID:25084974

  9. Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model

    Directory of Open Access Journals (Sweden)

    Beuf Kristof

    2012-11-01

    Full Text Available Abstract Background 454 pyrosequencing is a commonly used massively parallel DNA sequencing technology with a wide variety of application fields such as epigenetics, metagenomics and transcriptomics. A well-known problem of this platform is its sensitivity to base-calling insertion and deletion errors, particularly in the presence of long homopolymers. In addition, the base-call quality scores are not informative with respect to whether an insertion or a deletion error is more likely. Surprisingly, not much effort has been devoted to the development of improved base-calling methods and more intuitive quality scores for this platform. Results We present HPCall, a 454 base-calling method based on a weighted Hurdle Poisson model. HPCall uses a probabilistic framework to call the homopolymer lengths in the sequence by modeling well-known 454 noise predictors. Base-calling quality is assessed based on estimated probabilities for each homopolymer length, which are easily transformed to useful quality scores. Conclusions Using a reference data set of the Escherichia coli K-12 strain, we show that HPCall produces superior quality scores that are very informative towards possible insertion and deletion errors, while maintaining a base-calling accuracy that is better than the current one. Given the generality of the framework, HPCall has the potential to also adapt to other homopolymer-sensitive sequencing technologies.

  10. Sequencing-based variant detection in the polyploid crop oilseed rape

    Science.gov (United States)

    2013-01-01

    Background The detection and exploitation of genetic variation underpins crop improvement. However, the polyploid nature of the genomes of many of our most important crops represents a barrier, particularly for the analysis of variation within genes. To overcome this, we aimed to develop methodologies based on amplicon sequencing that involve the incorporation of barcoded amplification tags (BATs) into PCR products. Results A protocol was developed to tag PCR products with 5’ 6-base oligonucleotide barcode extensions before pooling for sequencing library production using standard Illumina adapters. A computational method was developed for the de-convolution of products and the robust detection and scoring of sequence variants. Using this methodology, amplicons targeted to gene sequences were screened across a B. napus mapping population and the resulting allele scoring strings for 24 markers linkage mapped to the expected regions of the genome. Furthermore, using one-dimensional 8-fold pooling, 4608 lines of a B. napus mutation population were screened for induced mutations in a locus-specific amplicon (an orthologue of GL2.b) and mixed product of three co-amplified loci (orthologues of FAD2), identifying 10 and 41 mutants respectively. Conclusions The utilisation of barcode tags to de-convolute pooled PCR products in multiplexed, variation screening via Illumina sequencing provides a cost effective method for SNP genotyping and mutation detection and, potentially, markers for causative changes, even in polyploid species. Combining this approach with existing Illumina multiplexing workflows allows the analysis of thousands of lines cheaply and efficiently in a single sequencing run with minimal library production costs. PMID:23915099

  11. Roche genome sequencer FLX based high-throughput sequencing of ancient DNA

    DEFF Research Database (Denmark)

    Alquezar-Planas, David E; Fordyce, Sarah Louise

    2012-01-01

    Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure tha...

  12. HomPPI: a class of sequence homology based protein-protein interface prediction methods

    Directory of Open Access Journals (Sweden)

    Dobbs Drena

    2011-06-01

    Full Text Available Abstract Background Although homology-based methods are among the most widely used methods for predicting the structure and function of proteins, the question as to whether interface sequence conservation can be effectively exploited in predicting protein-protein interfaces has been a subject of debate. Results We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence. Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i NPS-HomPPI (Non partner-specific HomPPI, which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii PS-HomPPI (Partner-specific HomPPI, which can be used to predict the interface residues of a query protein with a specific target protein. Our experiments on a benchmark dataset of obligate homodimeric complexes show that NPS-HomPPI can reliably predict protein-protein interface residues in a given protein, with an average correlation coefficient (CC of 0.76, sensitivity of 0.83, and specificity of 0.78, when sequence homologs of the query protein can be reliably identified. NPS-HomPPI also reliably predicts the interface residues of intrinsically disordered proteins. Our experiments suggest that NPS-HomPPI is competitive with several state-of-the-art interface prediction servers including those that exploit the structure of the query proteins. The partner-specific classifier, PS-HomPPI can, on a large dataset of transient complexes, predict the interface residues of a query protein with a specific target, with a CC of 0.65, sensitivity of 0.69, and specificity of 0.70, when homologs of

  13. Electronic band gaps and transport in aperiodic graphene-based superlattices of Thue-Morse sequence

    Science.gov (United States)

    Wang, Ligang; Ma, Tianxing

    2014-03-01

    We investigate electronic band structure and transport properties in aperiodic graphene-based superlattices of Thue-Morse (TM) sequence. The robust properties of zero- k gap are demonstrated in both mono-layer and bi-layer graphene TM sequence. The Extra Dirac points may emerge at ky ≠ 0, and the electronic transport behaviors such as the conductance and the Fano factor are discussed in detail. Our results provide a flexible and effective way to control the transport properties in graphene-based superlattices. This work is supported by NSFCs (Nos. 11274275, 11104014 and 61078021), Research Fund for the Doctoral Program of Higher Education 20110003120007, SRF for ROCS (SEM), and the National Basic Research Program of China (No. 2011CBA00108, and 2012CB921602).

  14. Data compression of discrete sequence: A tree based approach using dynamic programming

    Science.gov (United States)

    Shivaram, Gurusrasad; Seetharaman, Guna; Rao, T. R. N.

    1994-01-01

    A dynamic programming based approach for data compression of a ID sequence is presented. The compression of an input sequence of size N to that of a smaller size k is achieved by dividing the input sequence into k subsequences and replacing the subsequences by their respective average values. The partitioning of the input sequence is carried with the intention of reducing the mean squared error in the reconstructed sequence. The complexity involved in finding the partitions which would result in such an optimal compressed sequence is reduced by using the dynamic programming approach, which is presented.

  15. Sequence-based prediction of protein-peptide binding sites using support vector machine.

    Science.gov (United States)

    Taherzadeh, Ghazaleh; Yang, Yuedong; Zhang, Tuo; Liew, Alan Wee-Chung; Zhou, Yaoqi

    2016-05-15

    Protein-peptide interactions are essential for all cellular processes including DNA repair, replication, gene-expression, and metabolism. As most protein-peptide interactions are uncharacterized, it is cost effective to investigate them computationally as the first step. All existing approaches for predicting protein-peptide binding sites, however, are based on protein structures despite the fact that the structures for most proteins are not yet solved. This article proposes the first machine-learning method called SPRINT to make Sequence-based prediction of Protein-peptide Residue-level Interactions. SPRINT yields a robust and consistent performance for 10-fold cross validations and independent test. The most important feature is evolution-generated sequence profiles. For the test set (1056 binding and non-binding residues), it yields a Matthews' Correlation Coefficient of 0.326 with a sensitivity of 64% and a specificity of 68%. This sequence-based technique shows comparable or more accurate than structure-based methods for peptide-binding site prediction. SPRINT is available as an online server at: http://sparks-lab.org/. © 2016 Wiley Periodicals, Inc. PMID:26833816

  16. PHARMACOGENETIC TESTING OPPORTUNITIES IN CARDIOLOGY BASED ON EXOME SEQUENCING

    Directory of Open Access Journals (Sweden)

    N. V. Shcherbakova

    2015-09-01

    Full Text Available Aim. To study what cardiac drugs currently have any comments on biomarkers and what information can be obtained by pharmacogenetic testing using data exome sequencing in patients with cardiac diseases.Material and methods. Exome sequencing in random participant of the ATEROGEN IVANOVO study and bioinformatics analysis of the data were performed. Point mutations were annotated using ANNOVAR program, as well as comparison with a number of specialized databases was done on the basis of user protocols.Results. 11 cardiac drugs and 7 genes which variants can influence cardiac drug metabolism were analyzed. According to exome sequencing of the participant we did not reveal allelic variants that require dose regime correction and careful efficacy control.Conclusion. The exome sequencing application is the next step to a wide range of personalized therapy. Future opportunities for improvement of the risk-benefit ratio in each patient are the main purpose of the collection and analysis of pharmacogenetic data.

  17. Phylogenetic relationships of Salmonella based on rRNA sequences

    DEFF Research Database (Denmark)

    Christensen, H.; Nordentoft, Steen; Olsen, J.E.

    1998-01-01

    To establish the phylogenetic relationships between the subspecies of Salmonella enterica (official name Salmonella choleraesuis), Salmonella bongori and related members of Enterobacteriaceae, sequence comparison of rRNA was performed by maximum-likelihood analysis. The two Salmonella species were...

  18. Whole-genome sequence-based analysis of thyroid function

    DEFF Research Database (Denmark)

    Taylor, Peter N.; Porcu, Eleonora; Chew, Shelby;

    2015-01-01

    Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N = 2,287). Using additional whole-genome...... association with FT4 in NRG1. Our results demonstrate that increased coverage in whole-genome sequence association studies identifies novel variants associated with thyroid function....

  19. Test Case Generation Based on Use case and Sequence Diagram

    OpenAIRE

    Santosh Kumar Swain; Durga Prasad Mohapatra; Rajib Mall

    2010-01-01

    We present a comprehensive test case generation technique from UML models. We use the features in UML 2.0 sequence diagram including conditions, iterations, asynchronous messages and concurrent components. In our approach, test cases are derived from analysis artifacts such as use cases, their corresponding sequence diagrams and constraints specified across all these artifacts. We construct Use case Dependency Graph (UDG) from use case diagram and Concurrent Control Flow Graph (CCFG) from cor...

  20. SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics

    OpenAIRE

    Will, Sebastian; Otto, Christina; Miladi, Milad; Möhl, Mathias; Backofen, Rolf

    2015-01-01

    Motivation: RNA-Seq experiments have revealed a multitude of novel ncRNAs. The gold standard for their analysis based on simultaneous alignment and folding suffers from extreme time complexity of O ( n 6 ) . Subsequently, numerous faster ‘Sankoff-style’ approaches have been suggested. Commonly, the performance of such methods relies on sequence-based heuristics that restrict the search space to optimal or near-optimal sequence alignments; however, the accuracy of sequence-based methods breaks...

  1. Analysing humanly generated random number sequences: A pattern-based approach

    OpenAIRE

    Gravenor, M B; Schulz, M A; Schmalbach, B; Brugger, P; Witt, K.

    2012-01-01

    In a random number generation task, participants are asked to generate a random sequence of numbers, most typically the digits 1 to 9. Such number sequences are not mathematically random, and both extent and type of bias allow one to characterize the brain's “internal random number generator”. We assume that certain patterns and their variations will frequently occur in humanly generated random number sequences. Thus, we introduce a pattern-based analysis of random number sequences. Twenty he...

  2. Analysing Humanly Generated Random Number Sequences: A Pattern-Based Approach

    OpenAIRE

    Schulz, Marc-André; Schmalbach, Barbara; Brugger, Peter; Witt, Karsten

    2012-01-01

    In a random number generation task, participants are asked to generate a random sequence of numbers, most typically the digits 1 to 9. Such number sequences are not mathematically random, and both extent and type of bias allow one to characterize the brain's “internal random number generator”. We assume that certain patterns and their variations will frequently occur in humanly generated random number sequences. Thus, we introduce a pattern-based analysis of random number sequences. Twenty he...

  3. Changes in DNA base sequences in the mutant of Arabidopsis thaliana induced by low-energy N+ implantation

    Institute of Scientific and Technical Information of China (English)

    常凤启; 刘选明; 李银心; 贾庚祥; 马晶晶; 刘公社; 朱至清

    2003-01-01

    To reveal the mutation effect of low-energy ion implantation on Arabidopsis thaliana in vivo, T80II, a stable dwarf mutant, derived from the seeds irradiated by 30 keV N+ with the dose of 80×1015 ions/cm2 was used for Random Amplified Polymorphic DNA (RAPD) and base sequence analysis. The results indicated that among total 397 RAPD bands observed, 52 bands in T80II were different from those of wild type showing a variation frequency 13.1%. In comparison with the sequences of A. thaliana in GenBank, the RAPD fragments in T80II were changed greatly in base sequences with an average rate of one base change per 16.8 bases. The types of base changes included base transition, transversion, deletion and insertion. Among the 275 base changes detected, single base substitutions (97.09%) occurred more frequently than base deletions and insertions (2.91%). And the frequency of base transitions (66.55%) was higher than that of base transversions (30.55%). Adenine, thymine, guanine or cytosine could be replaced by any of other three bases in cloned DNA fragments in T80II. It seems that thymine was more sensitive to the irradiation than other bases. The flanking sequences of the base changes in RAPD fragments in T80II were analyzed and the mutational "hotspot" induced by low-energy ion implantation was discussed.

  4. Autonomously generating operations sequences for a Mars Rover using AI-based planning

    Science.gov (United States)

    Sherwood, Rob; Mishkin, Andrew; Estlin, Tara; Chien, Steve; Backes, Paul; Cooper, Brian; Maxwell, Scott; Rabideau, Gregg

    2001-01-01

    This paper discusses a proof-of-concept prototype for ground-based automatic generation of validated rover command sequences from highlevel science and engineering activities. This prototype is based on ASPEN, the Automated Scheduling and Planning Environment. This Artificial Intelligence (AI) based planning and scheduling system will automatically generate a command sequence that will execute within resource constraints and satisfy flight rules.

  5. The Research of Chaos-based M-ary Spreading Sequences

    Directory of Open Access Journals (Sweden)

    YANG Hongye

    2012-12-01

    Full Text Available This paper is devoted to the generation and evaluation of the Chaos-based M-ary spreading sequences on communications systems. Sequences obtained by repeating a truncated and multi-ary quantized chaotic series are compared with classical m-sequences by means of the autocorrelation and cross-correlation properties and power-spectral features. Anti-noise performance of binary sequences and chaotic-based M-ary spreading sequences has been compared in the case of the same single-frequency interferences. Studies have shown that spectral features and anti-noise performance of chaotic-based M-ary spreading sequences which have great researching value are better than binary sequences.

  6. Prediction of peptide drift time in ion mobility mass spectrometry from sequence-based features

    KAUST Repository

    Wang, Bing

    2013-05-09

    Background: Ion mobility-mass spectrometry (IMMS), an analytical technique which combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS), can rapidly separates ions on a millisecond time-scale. IMMS becomes a powerful tool to analyzing complex mixtures, especially for the analysis of peptides in proteomics. The high-throughput nature of this technique provides a challenge for the identification of peptides in complex biological samples. As an important parameter, peptide drift time can be used for enhancing downstream data analysis in IMMS-based proteomics.Results: In this paper, a model is presented based on least square support vectors regression (LS-SVR) method to predict peptide ion drift time in IMMS from the sequence-based features of peptide. Four descriptors were extracted from peptide sequence to represent peptide ions by a 34-component vector. The parameters of LS-SVR were selected by a grid searching strategy, and a 10-fold cross-validation approach was employed for the model training and testing. Our proposed method was tested on three datasets with different charge states. The high prediction performance achieve demonstrate the effectiveness and efficiency of the prediction model.Conclusions: Our proposed LS-SVR model can predict peptide drift time from sequence information in relative high prediction accuracy by a test on a dataset of 595 peptides. This work can enhance the confidence of protein identification by combining with current protein searching techniques. 2013 Wang et al.; licensee BioMed Central Ltd.

  7. A method to prioritize quantitative traits and individuals for sequencing in family-based studies.

    Directory of Open Access Journals (Sweden)

    Kaanan P Shah

    Full Text Available Owing to recent advances in DNA sequencing, it is now technically feasible to evaluate the contribution of rare variation to complex traits and diseases. However, it is still cost prohibitive to sequence the whole genome (or exome of all individuals in each study. For quantitative traits, one strategy to reduce cost is to sequence individuals in the tails of the trait distribution. However, the next challenge becomes how to prioritize traits and individuals for sequencing since individuals are often characterized for dozens of medically relevant traits. In this article, we describe a new method, the Rare Variant Kinship Test (RVKT, which leverages relationship information in family-based studies to identify quantitative traits that are likely influenced by rare variants. Conditional on nuclear families and extended pedigrees, we evaluate the power of the RVKT via simulation. Not unexpectedly, the power of our method depends strongly on effect size, and to a lesser extent, on the frequency of the rare variant and the number and type of relationships in the sample. As an illustration, we also apply our method to data from two genetic studies in the Old Order Amish, a founder population with extensive genealogical records. Remarkably, we implicate the presence of a rare variant that lowers fasting triglyceride levels in the Heredity and Phenotype Intervention (HAPI Heart study (p = 0.044, consistent with the presence of a previously identified null mutation in the APOC3 gene that lowers fasting triglyceride levels in HAPI Heart study participants.

  8. Load sequence effects on the fatigue of unnotched composite materials

    Science.gov (United States)

    Yang, J. N.; Jones, D. L.

    1981-01-01

    A more comprehensive version of an earlier fatigue and residual strength degradation model is proposed to predict the effect of load sequence on the statistical fatigue behavior of composite laminates. The model, which reduces to various fatigue models proposed in the literature by means of approximations, is verified by a survey of experiments on glass/epoxy laminates. It is shown that the correlation between the model and the test results under dual stress levels is reasonable, and that a simplified version of the model is verified by experiments on graphite/epoxy laminates in which the correlation between theoretical predictions and results under dual stress levels is satisfactory. The model is also shown capable of predicting the effect of proof loads on the fatigue behavior of composite materials.

  9. Novel Sequence Number Based Secure Authentication Scheme for Wireless LANs

    Institute of Scientific and Technical Information of China (English)

    Rajeev Singh; Teek Parval Sharma

    2015-01-01

    Authentication per frame is an implicit necessity for security in wireless local area networks (WLANs). We propose a novel per frame secure authentication scheme which provides authentication to data frames in WLANs. The scheme involves no cryptographic overheads for authentication of frames. It utilizes the sequence number of the frame along with the authentication stream generators for authentication. Hence, it requires no extra bits or messages for the authentication purpose and also no change in the existing frame format is required. The scheme provides authentication by modifying the sequence number of the frame at the sender, and that the modification is verified at the receiver. The modified sequence number is protected by using the XOR operation with a random number selected from the random stream. The authentication is lightweight due to the fact that it requires only trivial arithmetic operations like the subtraction and XOR operation.

  10. Predicting tissue-specific expressions based on sequence characteristics

    KAUST Repository

    Paik, Hyojung

    2011-04-30

    In multicellular organisms, including humans, understanding expression specificity at the tissue level is essential for interpreting protein function, such as tissue differentiation. We developed a prediction approach via generated sequence features from overrepresented patterns in housekeeping (HK) and tissue-specific (TS) genes to classify TS expression in humans. Using TS domains and transcriptional factor binding sites (TFBSs), sequence characteristics were used as indices of expressed tissues in a Random Forest algorithm by scoring exclusive patterns considering the biological intuition; TFBSs regulate gene expression, and the domains reflect the functional specificity of a TS gene. Our proposed approach displayed better performance than previous attempts and was validated using computational and experimental methods.

  11. A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Fei Chen

    2003-01-01

    Full Text Available DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT – the bionic wavelet transform (BWT – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the structural feature of the DNA sequence, was introduced into WT. It can adjust the weight value of each channel to maximise the useful energy distribution of the whole BWT output. The performance of the proposed BWT was examined by analysing synthetic and real DNA sequences. Results show that BWT performs better than traditional WT in presenting greater energy distribution. This new BWT method should be useful for the detection of the latent structural features in future DNA sequence analysis.

  12. Effect of Implantation Sequence on Tribological Behavior of GCr15 Steel by PBII

    Science.gov (United States)

    Gu, Le; Zhou, Hui; Cao, Guojian; Tang, Guangze; Ma, Xinxin; Wang, Liqin

    2016-05-01

    In the present work, the effect of implantation sequence on tribological behavior of GCr15 steel treated by plasma-based ion implantation of carbon and nitrogen has been investigated. The treated GCr15 steels were characterized for microstructure and abrasive wear performance through combination of Raman spectroscopy, nano-indentation, and wear tests. Raman spectroscopy indicated that diamond-like carbon (DLC) films were formed after implantation of carbon with or without implantation of nitrogen, and the implantation of nitrogen after the implantation of carbon destroyed the graphite structure of the DLC films. The nano-indentation and wear tests showed that nanohardness as well as wear resistance of the GCr15 steel treated with the implantation sequence of nitrogen-carbon was better than those with the implantation sequence of carbon-nitrogen. Meanwhile, the properties were improved with increasing of carbon ion fluence.

  13. Robin Sequence: The road to evidence based personalized treatment

    NARCIS (Netherlands)

    H. Basart

    2016-01-01

    Robin Sequence (RS) is characterized by micrognathia and upper airway obstruction (UAO) caused by glossoptosis resulting in respiratory and feeding problems of varying severity. According to the original RS definition a cleft palate is associated with RS, but not part of the definition. Reported inc

  14. Phylogenetic relationships of Salmonella based on rRNA sequences

    DEFF Research Database (Denmark)

    Christensen, H.; Nordentoft, Steen; Olsen, J.E.

    1998-01-01

    separated by 16S rRNA analysis and found to be closely related to the Escherichia coli and Shigella complex by both 16S and 23S rRNA analyses. The diphasic serotypes S. enterica subspp. I and VI were separated from the monophasic serotypes subspp. IIIa and IV, including S. bongori, by 23S rRNA sequence...

  15. Nonparametric density estimators based on nonstationary absolutely regular random sequences

    Directory of Open Access Journals (Sweden)

    Michel Harel

    1996-01-01

    Full Text Available In this paper, the central limit theorems for the density estimator and for the integrated square error are proved for the case when the underlying sequence of random variables is nonstationary. Applications to Markov processes and ARMA processes are provided.

  16. A fast sequence assembly method based on compressed data structures.

    Science.gov (United States)

    Liang, Peifeng; Zhang, Yancong; Lin, Kui; Hu, Jinglu

    2014-01-01

    Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these requirements, a memory and time efficient assembler is presented from applying FM-index in JR-Assembler, called FMJ-Assembler, where FM stand for FMR-index derived from the FM-index and BWT and J for jumping extension. The FMJ-Assembler uses expanded FM-index and BWT to compress data of reads to save memory and jumping extension method make it faster in CPU time. An extensive comparison of the FMJ-Assembler with current assemblers shows that the FMJ-Assembler achieves a better or comparable overall assembly quality and requires lower memory use and less CPU time. All these advantages of the FMJ-Assembler indicate that the FMJ-Assembler will be an efficient assembly method in next generation sequencing technology. PMID:25569963

  17. Phylogeny of Vibrio cholerae Based on recA Sequence

    OpenAIRE

    Stine, O. Colin; Sozhamannan, Shanmuga; Gou, Qing; Zheng, Siqen; Morris, J. Glenn; Johnson, Judith A.

    2000-01-01

    We sequenced a 705-bp fragment of the recA gene from 113 Vibrio cholerae strains and closely related species. One hundred eighty-seven nucleotides were phylogenetically informative, 55 were phylogenetically uninformative, and 463 were invariant. Not unexpectedly, Vibrio parahaemolyticus and Vibrio vulnificus strains formed out-groups; we also identified isolates which resembled V. cholerae biochemically but which did not cluster with V. cholerae. In many instances, V. cholerae serogroup desig...

  18. Evolutionary insights from suffix array-based genome sequence analysis

    Indian Academy of Sciences (India)

    Anindya Poddar; Nagasuma Chandra; Madhavi Ganapathiraju; K Sekar; Judith Klein-Seetharaman; Raj Reddy; N Balakrishnan

    2007-08-01

    Gene and protein sequence analyses, central components of studies in modern biology are easily amenable to string matching and pattern recognition algorithms. The growing need of analysing whole genome sequences more efficiently and thoroughly, has led to the emergence of new computational methods. Suffix trees and suffix arrays are data structures, well known in many other areas and are highly suited for sequence analysis too. Here we report an improvement to the design of construction of suffix arrays. Enhancement in versatility and scalability, enabled by this approach, is demonstrated through the use of real-life examples. The scalability of the algorithm to whole genomes renders it suitable to address many biologically interesting problems. One example is the evolutionary insight gained by analysing unigrams, bi-grams and higher n-grams, indicating that the genetic code has a direct influence on the overall composition of the genome. Further, different proteomes have been analysed for the coverage of the possible peptide space, which indicate that as much as a quarter of the total space at the tetra-peptide level is left un-sampled in prokaryotic organisms, although almost all tri-peptides can be seen in one protein or another in a proteome. Besides, distinct patterns begin to emerge for the counts of particular tetra and higher peptides, indicative of a ‘meaning’ for tetra and higher n-grams. The toolkit has also been used to demonstrate the usefulness of identifying repeats in whole proteomes efficiently. As an example, 16 members of one COG, coded by the genome of Mycobacterium tuberculosis H37Rv have been found to contain a repeating sequence of 300 amino acids.

  19. INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences

    OpenAIRE

    Mohammed, Monzoorul Haque; Ghosh, Tarini Shankar; Reddy, Rachamalla Maheedhar; Reddy, Chennareddy Venkata Siva Kumar; Singh, Nitin Kumar; Sharmila S Mande

    2011-01-01

    Background Taxonomic classification of metagenomic sequences is the first step in metagenomic analysis. Existing taxonomic classification approaches are of two types, similarity-based and composition-based. Similarity-based approaches, though accurate and specific, are extremely slow. Since, metagenomic projects generate millions of sequences, adopting similarity-based approaches becomes virtually infeasible for research groups having modest computational resources. In this study, we present ...

  20. Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution

    Indian Academy of Sciences (India)

    S Balaji; N Srinivasan

    2007-01-01

    Several studies based on the known three-dimensional (3-D) structures of proteins show that two homologous proteins with insignificant sequence similarity could adopt a common fold and may perform same or similar biochemical functions. Hence, it is appropriate to use similarities in 3-D structure of proteins rather than the amino acid sequence similarities in modelling evolution of distantly related proteins. Here we present an assessment of using 3-D structures in modelling evolution of homologous proteins. Using a dataset of 108 protein domain families of known structures with at least 10 members per family we present a comparison of extent of structural and sequence dissimilarities among pairs of proteins which are inputs into the construction of phylogenetic trees. We find that correlation between the structure-based dissimilarity measures and the sequence-based dissimilarity measures is usually good if the sequence similarity among the homologues is about 30% or more. For protein families with low sequence similarity among the members, the correlation coefficient between the sequence-based and the structure-based dissimilarities are poor. In these cases the structure-based dendrogram clusters proteins with most similar biochemical functional properties better than the sequence-similarity based dendrogram. In multi-domain protein families and disulphide-rich protein families the correlation coefficient for the match of sequence-based and structure-based dissimilarity (SDM) measures can be poor though the sequence identity could be higher than 30%. Hence it is suggested that protein evolution is best modelled using 3-D structures if the sequence similarities (SSM) of the homologues are very low.

  1. DNA Lossless Differential Compression Algorithm based on Similarity of Genomic Sequence Database

    CERN Document Server

    Afify, Heba; Wahed, Manal Abdel

    2011-01-01

    Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information theory are often perceived as being of interest for data communication and storage. In recent years, a substantial effort has been made for the application of textual data compression techniques to various computational biology tasks, ranging from storage and indexing of large datasets to comparison of genomic databases. This paper presents a differential compression algorithm that is based on production of difference sequences according to op-code table in order to optimize the compression of homologous sequences in dataset. Therefore, the stored data are composed of reference sequence, the set of differences, and differences locations, instead of storing each sequence individually. This algorithm does not require a priori knowledge about the statistics of the sequence set. The...

  2. A Parallel Non-Alignment Based Approach to Efficient Sequence Comparison using Longest Common Subsequences

    Science.gov (United States)

    Bhowmick, S.; Shafiullah, M.; Rai, H.; Bastola, D.

    2010-11-01

    Biological sequence comparison programs have revolutionized the practice of biochemistry, and molecular and evolutionary biology. Pairwise comparison of genomic sequences is a popular method of choice for analyzing genetic sequence data. However the quality of results from most sequence comparison methods are significantly affected by small perturbations in the data and furthermore, there is a dearth of computational tools to compare sequences beyond a certain length. In this paper, we describe a parallel algorithm for comparing genetic sequences using an alignment free-method based on computing the Longest Common Subsequence (LCS) between genetic sequences. We validate the quality of our results by comparing the phylogenetic tress obtained from ClustalW and LCS. We also show through complexity analysis of the isoefficiency and by empirical measurement of the running time that our algorithm is very scalable.

  3. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.

    Science.gov (United States)

    Drmanac, Radoje; Sparks, Andrew B; Callow, Matthew J; Halpern, Aaron L; Burns, Norman L; Kermani, Bahram G; Carnevali, Paolo; Nazarenko, Igor; Nilsen, Geoffrey B; Yeung, George; Dahl, Fredrik; Fernandez, Andres; Staker, Bryan; Pant, Krishna P; Baccash, Jonathan; Borcherding, Adam P; Brownley, Anushka; Cedeno, Ryan; Chen, Linsu; Chernikoff, Dan; Cheung, Alex; Chirita, Razvan; Curson, Benjamin; Ebert, Jessica C; Hacker, Coleen R; Hartlage, Robert; Hauser, Brian; Huang, Steve; Jiang, Yuan; Karpinchyk, Vitali; Koenig, Mark; Kong, Calvin; Landers, Tom; Le, Catherine; Liu, Jia; McBride, Celeste E; Morenzoni, Matt; Morey, Robert E; Mutch, Karl; Perazich, Helena; Perry, Kimberly; Peters, Brock A; Peterson, Joe; Pethiyagoda, Charit L; Pothuraju, Kaliprasad; Richter, Claudia; Rosenbaum, Abraham M; Roy, Shaunak; Shafto, Jay; Sharanhovich, Uladzislau; Shannon, Karen W; Sheppy, Conrad G; Sun, Michel; Thakuria, Joseph V; Tran, Anne; Vu, Dylan; Zaranek, Alexander Wait; Wu, Xiaodi; Drmanac, Snezana; Oliphant, Arnold R; Banyai, William C; Martin, Bruce; Ballinger, Dennis G; Church, George M; Reid, Clifford A

    2010-01-01

    Genome sequencing of large numbers of individuals promises to advance the understanding, treatment, and prevention of human diseases, among other applications. We describe a genome sequencing platform that achieves efficient imaging and low reagent consumption with combinatorial probe anchor ligation chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs. We sequenced three human genomes with this platform, generating an average of 45- to 87-fold coverage per genome and identifying 3.2 to 4.5 million sequence variants per genome. Validation of one genome data set demonstrates a sequence accuracy of about 1 false variant per 100 kilobases. The high accuracy, affordable cost of $4400 for sequencing consumables, and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies. PMID:19892942

  4. Cluster-Based Multipolling Sequencing Algorithm for Collecting RFID Data in Wireless LANs

    Science.gov (United States)

    Choi, Woo-Yong; Chatterjee, Mainak

    2015-03-01

    With the growing use of RFID (Radio Frequency Identification), it is becoming important to devise ways to read RFID tags in real time. Access points (APs) of IEEE 802.11-based wireless Local Area Networks (LANs) are being integrated with RFID networks that can efficiently collect real-time RFID data. Several schemes, such as multipolling methods based on the dynamic search algorithm and random sequencing, have been proposed. However, as the number of RFID readers associated with an AP increases, it becomes difficult for the dynamic search algorithm to derive the multipolling sequence in real time. Though multipolling methods can eliminate the polling overhead, we still need to enhance the performance of the multipolling methods based on random sequencing. To that extent, we propose a real-time cluster-based multipolling sequencing algorithm that drastically eliminates more than 90% of the polling overhead, particularly so when the dynamic search algorithm fails to derive the multipolling sequence in real time.

  5. Combined sequence and sequence-structure based methods for analyzing FGF23, CYP24A1 and VDR genes.

    Science.gov (United States)

    Nagamani, Selvaraman; Singh, Kh Dhanachandra; Muthusamy, Karthikeyan

    2016-09-01

    FGF23, CYP24A1 and VDR altogether play a significant role in genetic susceptibility to chronic kidney disease (CKD). Identification of possible causative mutations may serve as therapeutic targets and diagnostic markers for CKD. Thus, we adopted both sequence and sequence-structure based SNP analysis algorithm in order to overcome the limitations of both methods. We explore the functional significance towards the prediction of risky SNPs associated with CKD. We assessed the performance of four widely used pathogenicity prediction methods. We compared the performances of the programs using Mathews correlation Coefficient ranged from poor (MCC = 0.39) to reasonably good (MCC = 0.42). However, we got the best results for the combined sequence and structure based analysis method (MCC = 0.45). 4 SNPs from FGF23 gene, 8 SNPs from VDR gene and 13 SNPs from CYP24A1 gene were predicted to be the causative agents for human diseases. This study will be helpful in selecting potential SNPs for experimental study from the SNP pool and also will reduce the cost for identification of potential SNPs as a genetic marker. PMID:27114920

  6. Parallel divide and conquer bio-sequence comparison based on Smith-Waterman algorithm

    Institute of Scientific and Technical Information of China (English)

    ZHANG Fa; QIAO Xiangzhen; LIU Zhiyong

    2004-01-01

    Tools for pair-wise bio-sequence alignment have for long played a central role in computation biology. Several algorithms for bio-sequence alignment have been developed. The Smith-Waterman algorithm, based on dynamic programming, is considered the most fundamental alignment algorithm in bioinformatics. However the existing parallel Smith-Waterman algorithm needs large memory space, and this disadvantage limits the size of a sequence to be handled. As the data of biological sequences expand rapidly, the memory requirement of the existing parallel SmithWaterman algorithm has become a critical problem. For solving this problem, we develop a new parallel bio-sequence alignment algorithm, using the strategy of divide and conquer, named PSW-DC algorithm. In our algorithm, first, we partition the query sequence into several subsequences and distribute them to every processor respectively,then compare each subsequence with the whole subject sequence in parallel, using the Smith-Waterman algorithm, and get an interim result, finally obtain the optimal alignment between the query sequence and subject sequence, through the special combination and extension method. Memory space required in our algorithm is reduced significantly in comparison with existing ones. We also develop a key technique of combination and extension, named the C&E method, to manipulate the interim results and obtain the final sequences alignment. We implement the new parallel bio-sequences alignment algorithm,the PSW-DC, in a cluster parallel system.

  7. Readjoiner: a fast and memory efficient string graph-based sequence assembler

    OpenAIRE

    Gonnella Giorgio; Kurtz Stefan

    2012-01-01

    Abstract Background Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction of a de Bruijn graph. An alternative framework of growing interest is the assembly string graph, not necessitating a division of the reads into k-mers, but requiring fast algorithms for the computation of suffix-prefix matches among all pairs of reads. Results Here we...

  8. LookSeq: A browser-based viewer for deep sequencing data

    OpenAIRE

    Manske, Heinrich Magnus; Dominic P Kwiatkowski

    2009-01-01

    Sequencing a genome to great depth can be highly informative about heterogeneity within an individual or a population. Here we address the problem of how to visualize the multiple layers of information contained in deep sequencing data. We propose an interactive AJAX-based web viewer for browsing large data sets of aligned sequence reads. By enabling seamless browsing and fast zooming, the LookSeq program assists the user to assimilate information at different levels of resolution, from an ov...

  9. Improved Channel Estimation Methods based on PN sequence for TDS-OFDM

    OpenAIRE

    Liu, Ming; Crussière, Matthieu; Hélard, Jean-François

    2012-01-01

    An accurate channel estimation is crucial for the novel time domain synchronous orthogonal frequency-division multiplexing (TDS-OFDM) scheme in which pseudo noise (PN) sequences serve as both guard intervals (GI) for OFDM data symbols and training sequences for synchronization/channel estimation. This paper studies the channel estimation method based on the cross-correlation of PN sequences. A theoretical analysis of this estimator is conducted and several improved estimators are then propose...

  10. A Word Extraction Method from Newspaper Articles Based on Time Infomation for Event Sequence Mining

    Science.gov (United States)

    Tada, Tomomichi; Iwanuma, Koji; Nabeshima, Hidetomo

    This paper shows a new method of extracting important words from newspaper articles based on time-sequence information. This word extraction method plays an important role in event sequence mining. TF-IDF is a well-known method to rank word's importance in a document. However, the TF-IDF method never consider the time information embedded in sequential textual data, which is peculiar to newspapers. In this research, we will propose a new word-extraction method, called the TF-IDayF method, which considers time-sequence information, and can extract important/characteristic words expressing sequential events. The TF-IDayF method never use so-called burst phenomenon of topic word occurrences, which has been studied by lots of researchers. The TF-IDayF method is quite simple, but effective and easy to compute in sequential textual mining. We evaluate the proposed method from three points of view, i.e., a semantic viewpoint, a statistical one and a data mining viewpoint through several experiments.

  11. Dissecting the roles of local packing density and longer-range effects in protein sequence evolution

    CERN Document Server

    Shahmoradi, Amir

    2015-01-01

    What are the structural determinants of protein sequence evolution? A number of site-specific structural characteristics have been proposed, most of which are broadly related to either the density of contacts or the solvent accessibility of individual residues. Most importantly, there has been disagreement in the literature over the relative importance of solvent accessibility and local packing density for explaining site-specific sequence variability in proteins. We show here that this discussion has been confounded by the definition of local packing density. The most commonly used measures of local packing, such as the contact number and the weighted contact number, represent by definition the combined effects of local packing density and longer-range effects. As an alternative, we here propose a truly local measure of packing density around a single residue, based on the Voronoi cell volume. We show that the Voronoi cell volume, when calculated relative to the geometric center of amino-acid side chains, be...

  12. Mining of haplotype-based expressed sequence tag single nucleotide polymorphisms in citrus

    OpenAIRE

    Chen, Chunxian; Gmitter Jr, Fred G

    2013-01-01

    Background Single nucleotide polymorphisms (SNPs), the most abundant variations in a genome, have been widely used in various studies. Detection and characterization of citrus haplotype-based expressed sequence tag (EST) SNPs will greatly facilitate further utilization of these gene-based resources. Results In this paper, haplotype-based SNPs were mined out of publicly available citrus expressed sequence tags (ESTs) from different citrus cultivars (genotypes) individually and collectively for...

  13. Sequence-Length Requirement of Distance-Based Phylogeny Reconstruction: Breaking the Polynomial Barrier

    CERN Document Server

    Roch, Sebastien

    2009-01-01

    We introduce a new distance-based phylogeny reconstruction technique which provably achieves, at sufficiently short branch lengths, a polylogarithmic sequence-length requirement -- improving significantly over previous polynomial bounds for distance-based methods. The technique is based on an averaging procedure that implicitly reconstructs ancestral sequences. In the same token, we extend previous results on phase transitions in phylogeny reconstruction to general time-reversible models. More precisely, we show that in the so-called Kesten-Stigum zone (roughly, a region of the parameter space where ancestral sequences are well approximated by ``linear combinations'' of the observed sequences) sequences of length $\\poly(\\log n)$ suffice for reconstruction when branch lengths are discretized. Here $n$ is the number of extant species. Our results challenge, to some extent, the conventional wisdom that estimates of evolutionary distances alone carry significantly less information about phylogenies than full sequ...

  14. High-Throughput Sequencing Based Methods of RNA Structure Investigation

    DEFF Research Database (Denmark)

    Kielpinski, Lukasz Jan

    In this thesis we describe the development of four related methods for RNA structure probing that utilize massive parallel sequencing. Using them, we were able to gather structural data for multiple, long molecules simultaneously. First, we have established an easy to follow experimental and...... RTTS-Seq to detect antisense oligonucleotide binding sites within a transcriptome. In this case, we applied an enrichment strategy to greatly reduce the background. Finally, we have modified the RTTS-Seq to study the secondary structure of 3’ untranslated regions. In the course of this thesis we...... computational protocol for detecting the reverse transcription termination sites (RTTS-Seq). This protocol was subsequently applied to hydroxyl radical footprinting of three dimensional RNA structures to give a probing signal that correlates well with the RNA backbone solvent accessibility. Moreover, we applied...

  15. A method for amplification of unknown flanking sequences based on touchdown PCR and suppression-PCR.

    Science.gov (United States)

    Gao, Song; He, Dan; Li, Guangquan; Zhang, Yanhua; Lv, Huiying; Wang, Li

    2016-09-15

    Thermal asymmetric staggered PCR is the most widely used technique to obtain the flanking sequences. However, it has some limitations, including a low rate of positivity, and complex operation. In this study, a improved method of it was made based on suppression-PCR and touchdown PCR. The PCR fragment obtained by the amplification was used directly for sequencing after gel purification. Using this improved method, the positive rate of amplified flanking sequences of the ATMT mutants reached 99%. In addition, the time from DNA extraction to flanking sequence analysis was shortened to 2 days with about 6 dollars each sample. PMID:27393656

  16. An Approach to Assembly Sequence Plannning Based on Hierarchical Strategy and Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    Niu Xinwen; Ding Han; Xiong Youlun

    2001-01-01

    Using group and subassembly cluster methods, the hierarchical structure of a product is.generated automatically, which largely reduces the complexity of planning. Based on genetic algofithn the optimal of assembly sequence of each stracture level can be obtained by sequence-bysequence search. As a result, a better assembly sequence of the product can be generated by combining the assembly sequences of all hierarchical structures, which provides more parallelism and flexibility for assembly operations. An industrial example is solved by this new approach.

  17. THE CONSTRUCTIONS OF ALMOST BINARY SEQUENCE PAIRS WITH THREE-LEVEL CORRELATION BASED ON CYCLOTOMY

    Institute of Scientific and Technical Information of China (English)

    Peng Xiuping; Xu Chengqian

    2012-01-01

    In this paper,a new class of almost binary sequence pair with a single zero element is presented.The almost binary sequence pairs with three-level correlation are constructed based on cyclotomic numbers of order 2,4,and 6.Most of them have good correlation and balance property,whose maximum nontrivial correlation magnitudes are 2 and the difference between the numbers of occurrence of +1's and -1's are 0 or 1.In addition,the corresponding binary sequence pairs are investigated as well and we can also get some kinds of binary sequence pairs with optimum balance and good correlation.

  18. EFFECT OF DYE CONCENTRATION ON SEQUENCING BATCH REACTOR PERFORMANCE

    Directory of Open Access Journals (Sweden)

    A. A. Vaigan ، M. R. Alavi Moghaddam ، H. Hashemi

    2009-01-01

    Full Text Available Reactive dyes have been identified as problematic compounds in textile industries wastewater as they are water soluble and cannot be easily removed by conventional aerobic biological treatment systems. The treatability of a reactive dye (Brill Blue KN-R by sequencing batch reactor and the influence of the dye concentration on system performance were investigated in this study. Brill Blue KN-R is one of the main dyes that are used in textile industries in Iran. Four cylindrical Plexiglas reactors were run for 36 days (5 days for acclimatization of sludge and 31 days for normal operation at different initial dye concentrations. The dye concentrations were adjusted to be 20, 25, 30 and 40 mg/L in the reactors R1, R2, R3 and R4, respectively. In all reactors, effective volume, influent wastewater flowrate and sludge retention time were 5.5 L, 3.0 L/d and 10 d, respectively. According to the obtained data, average dye removal efficiencies of R1, R2, R3 and R4 were 57% ± 2, 50.18% ± 3, 44.97% ± 3 and 30.98% ± 3, respectively. The average COD removal efficiencies of all reactors were 97% ± 1, 97.12% ± 1, 96.93% ± 1 and 97.22% ± 1, respectively. The dye removal efficiency was decreased by increasing the dye concentration with the correlation coefficient of 0.997.

  19. Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads

    Science.gov (United States)

    2016-01-01

    Motivation. The third generation sequencing (3GS) technology generates long sequences of thousands of bases. However, its current error rates are estimated in the range of 15–40%, significantly higher than those of the prevalent next generation sequencing (NGS) technologies (less than 1%). Fundamental bioinformatics tasks such as de novo genome assembly and variant calling require high-quality sequences that need to be extracted from these long but erroneous 3GS sequences. Results. We describe a versatile and efficient linear complexity consensus algorithm Sparc to facilitate de novo genome assembly. Sparc builds a sparse k-mer graph using a collection of sequences from a targeted genomic region. The heaviest path which approximates the most likely genome sequence is searched through a sparsity-induced reweighted graph as the consensus sequence. Sparc supports using NGS and 3GS data together, which leads to significant improvements in both cost efficiency and computational efficiency. Experiments with Sparc show that our algorithm can efficiently provide high-quality consensus sequences using both PacBio and Oxford Nanopore sequencing technologies. With only 30× PacBio data, Sparc can reach a consensus with error rate NGS data. Compared with the existing approaches, Sparc calculates the consensus with higher accuracy, and uses approximately 80% less memory and time. Availability. The source code is available for download at https://github.com/yechengxi/Sparc. PMID:27330851

  20. Molecular phylogeny of endophytic isolates of Ampelomyces from Iran based on rDNA ITS sequences.

    Science.gov (United States)

    Jamali, Samad

    2015-01-01

    During 2012, five isolates of pycnidial fungi were recovered from roots of tomato (Solanum lycopersicum) plants in Iran. Based on morphological characteristics the presence of Ampelomyces was documented. To confirm morphological identification and clarify the placement of endophytic isolates of Ampelomyces, DNA was extracted from isolates using a genomic DNA purification Kit. Region of internal transcribed spacers 1, 2 and 5.8S genes of rDNA were amplified using ITS4 and ITS1 universal primer set. Amplicons were purified, sequenced and submitted to the GenBank. The resulting sequence (600 bp) was submitted to a BLAST search to find most similar sequences in GenBank. The ITS sequences of isolates obtained in Iran were compared to those of other related authentic sequences obtained from GenBank. Iranian endophytic isolates had 100 % similarity of among themselves, while all isolates of Ampelomyces sequences analyzed had an average of 95.2 % (range 87-100 %) similarity. When Ampelomyces ITS sequences were analyzed by both distance-based and maximum parsimony methods, the Ampelomyces isolates were segregate into 11 distinct clades. The ITS sequences of endophytic isolates obtained in Iran were identical with endophytic isolates from other country including USA, Australia, Hungary and Spain. Our analyses of phylogenetic data showed that endophytic isolates from Iran and other countries are distinct group. The high ITS sequence-divergence values and the phylogenetic analysis suggested the isolates of Ampelomyces in the clades are not closely related and indeed a problematic species complex. PMID:25245955

  1. High-throughput-sequencing-based identification of a grapevine fanleaf virus satellite RNA in Vitis vinifera.

    Science.gov (United States)

    Chiumenti, Michela; Mohorianu, Irina; Roseti, Vincenzo; Saldarelli, Pasquale; Dalmay, Tamas; Minafra, Angelantonio

    2016-05-01

    A new satellite RNA (satRNA) of grapevine fanleaf virus (GFLV) was identified by high-throughput sequencing of high-definition (HD) adapter libraries from grapevine plants of the cultivar Panse precoce (PPE) affected by enation disease. The complete nucleotide sequence was obtained by automatic sequencing using primers designed based on next-generation sequencing (NGS) data. The full-length sequence, named satGFLV-PPE, consisted of 1119 nucleotides with a single open reading frame from position 15 to 1034. This satRNA showed maximum nucleotide sequence identity of 87 % to satArMV-86 and satGFLV-R6. Symptomatic grapevines were surveyed for the presence of the satRNA, and no correlation was found between detection of the satRNA and enation symptom expression. PMID:26873812

  2. CAPS satellite spread spectrum communication blind multi-user detecting system based on chaotic sequences

    Institute of Scientific and Technical Information of China (English)

    LEI LiHua; SHI HuLi; MA GuanYi

    2009-01-01

    Multiple Path Interference (MPI) and Multiple Access Interference (MAI) are Important factors that affect the performance of Chinese Area Positioning System (CAPS),These problems can be solved by using spreading sequences with ideal properties and multi-user detectors.Chaotic sequences based on Chebyshev map are studied and the satellite communication system model is set up to investigate the application of chaotic sequences for CAPS in this paper,Simulation results show that chaotic sequences have desirable correlation properties and it is easy to generate a large number of chaotic sequences with good security.It has great practical value to apply chaotic sequences to CAPS together with multi-user detecting technology and the system performance can be improved greatly.

  3. Approaches to the detection of recessive effects using next generation sequencing data from outbred populations

    Directory of Open Access Journals (Sweden)

    Curtis

    2013-06-01

    Full Text Available David Curtis Centre for Psychiatry, Barts and the London School of Medicine and Dentistry, London, UK Abstract: Conventional methods to analyze genome-wide association studies and whole exome or whole genome sequencing studies would be prone to overlook variants which might exert a recessive effect on risk of disease, either as homozygotes or compound heterozygotes. It is plausible that such effects may be common even in outbred populations. An approach is described which is based on identifying a set of variants in a gene as being potentially of interest and then testing whether there is an excess of cases who are either homozygotes or complex heterozygotes for these variants. Methods based on departure from Hardy–Weinberg equilibrium are more powerful than those which compare cases to controls. However, linkage disequilibrium between variants can be difficult to deal with if phase is unknown. A simple approach for discarding variants apparently in strong linkage disequilibrium with others is proposed. The procedure is simple and quick to apply so can be used in the context of whole genome or exome sequencing studies and is implemented in the SCOREASSOC program. Keywords: association, sequence, DNA

  4. Study on multiple-hops performance of MOOC sequences-based optical labels for OPS networks

    Science.gov (United States)

    Zhang, Chongfu; Qiu, Kun; Ma, Chunli

    2009-11-01

    In this paper, we utilize a new study method that is under independent case of multiple optical orthogonal codes to derive the probability function of MOOCS-OPS networks, discuss the performance characteristics for a variety of parameters, and compare some characteristics of the system employed by single optical orthogonal code or multiple optical orthogonal codes sequences-based optical labels. The performance of the system is also calculated, and our results verify that the method is effective. Additionally it is found that performance of MOOCS-OPS networks would, negatively, be worsened, compared with single optical orthogonal code-based optical label for optical packet switching (SOOC-OPS); however, MOOCS-OPS networks can greatly enlarge the scalability of optical packet switching networks.

  5. Control allocation and management of redundant control effectors based on bases sequenced optimal method

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    For an advanced aircraft, the amount of its effectors is much more than that for a traditional one, the functions of effectors are more complex and the coupling between each other is more severe. Based on the current control allocation research, this paper puts forward the concept and framework of the control allocation and management system for aircrafts with redundancy con-trol effectors. A new optimal control allocation method, bases sequenced optimal (BSO) method, is then presented. By analyz-ing the physical meaning of the allocation process of BSO method, four types of management strategies are adopted by the system, which act on the control allocation process under different flight conditions, mission requirements and effectors work-ing conditions. Simulation results show that functions of the control allocation system are extended and the system adaptability to flight status, mission requirements and effector failure conditions is improved.

  6. Improved PCR-Based Detection of Soil Transmitted Helminth Infections Using a Next-Generation Sequencing Approach to Assay Design

    Science.gov (United States)

    Pilotte, Nils; Papaiakovou, Marina; Grant, Jessica R.; Bierwert, Lou Ann; Llewellyn, Stacey; McCarthy, James S.; Williams, Steven A.

    2016-01-01

    Background The soil transmitted helminths are a group of parasitic worms responsible for extensive morbidity in many of the world’s most economically depressed locations. With growing emphasis on disease mapping and eradication, the availability of accurate and cost-effective diagnostic measures is of paramount importance to global control and elimination efforts. While real-time PCR-based molecular detection assays have shown great promise, to date, these assays have utilized sub-optimal targets. By performing next-generation sequencing-based repeat analyses, we have identified high copy-number, non-coding DNA sequences from a series of soil transmitted pathogens. We have used these repetitive DNA elements as targets in the development of novel, multi-parallel, PCR-based diagnostic assays. Methodology/Principal Findings Utilizing next-generation sequencing and the Galaxy-based RepeatExplorer web server, we performed repeat DNA analysis on five species of soil transmitted helminths (Necator americanus, Ancylostoma duodenale, Trichuris trichiura, Ascaris lumbricoides, and Strongyloides stercoralis). Employing high copy-number, non-coding repeat DNA sequences as targets, novel real-time PCR assays were designed, and assays were tested against established molecular detection methods. Each assay provided consistent detection of genomic DNA at quantities of 2 fg or less, demonstrated species-specificity, and showed an improved limit of detection over the existing, proven PCR-based assay. Conclusions/Significance The utilization of next-generation sequencing-based repeat DNA analysis methodologies for the identification of molecular diagnostic targets has the ability to improve assay species-specificity and limits of detection. By exploiting such high copy-number repeat sequences, the assays described here will facilitate soil transmitted helminth diagnostic efforts. We recommend similar analyses when designing PCR-based diagnostic tests for the detection of other

  7. A comparison of single molecule and amplification based sequencing of cancer transcriptomes.

    Directory of Open Access Journals (Sweden)

    Lee T Sam

    Full Text Available The second wave of next generation sequencing technologies, referred to as single-molecule sequencing (SMS, carries the promise of profiling samples directly without employing polymerase chain reaction steps used by amplification-based sequencing (AS methods. To examine the merits of both technologies, we examine mRNA sequencing results from single-molecule and amplification-based sequencing in a set of human cancer cell lines and tissues. We observe a characteristic coverage bias towards high abundance transcripts in amplification-based sequencing. A larger fraction of AS reads cover highly expressed genes, such as those associated with translational processes and housekeeping genes, resulting in relatively lower coverage of genes at low and mid-level abundance. In contrast, the coverage of high abundance transcripts plateaus off using SMS. Consequently, SMS is able to sequence lower- abundance transcripts more thoroughly, including some that are undetected by AS methods; however, these include many more mapping artifacts. A better understanding of the technical and analytical factors introducing platform specific biases in high throughput transcriptome sequencing applications will be critical in cross platform meta-analytic studies.

  8. VLSI Floorplanning with Boundary Constraints Based on Single-Sequence Representation

    Science.gov (United States)

    Li, Kang; Yu, Juebang; Li, Jian

    In modern VLSI physical design, huge integration scale necessitates hierarchical design and IP reuse to cope with design complexity. Besides, interconnect delay becomes dominant to overall circuit performance. These critical factors require some modules to be placed along designated boundaries to effectively facilitate hierarchical design and interconnection optimization related problems. In this paper, boundary constraints of general floorplan are solved smoothly based on the novel representation Single-Sequence (SS). Necessary and sufficient conditions of rooms along specified boundaries of a floorplan are proposed and proved. By assigning constrained modules to proper boundary rooms, our proposed algorithm always guarantees a feasible SS code with appropriate boundary constraints in each perturbation. Time complexity of the proposed algorithm is O(n). Experimental results on MCNC benchmarks show effectiveness and efficiency of the proposed method.

  9. How effective is graphene nanopore geometry on DNA sequencing?

    OpenAIRE

    Satarifard, Vahid; Foroutan, Masumeh; Ejtehadi, Mohammad Reza

    2015-01-01

    In this paper we investigate the effects of graphene nanopore geometry on homopolymer ssDNA pulling process through nanopore using steered molecular dynamic (SMD) simulations. Different graphene nanopores are examined including axially symmetric and asymmetric monolayer graphene nanopores as well as five layer graphene polyhedral crystals (GPC). The pulling force profile, moving fashion of ssDNA, work done in irreversible DNA pulling and orientations of DNA bases near the nanopore are assesse...

  10. Group Graded Associated Ideals with Flat Base Change of Rings and Short Exact Sequences

    Indian Academy of Sciences (India)

    Srinivas Behara; Shiv Datt Kumar

    2011-05-01

    This paper deals with the study of behaviour of -associated ideals and strong Krull -associated ideals with flat base change of rings and behaviour of -associated ideals with short exact sequences over rings graded by finitely generated abelian group .

  11. Design and Evaluation of a Research-Based Teaching Sequence: The Superposition of Electric Field.

    Science.gov (United States)

    Viennot, L.; Rainson, S.

    1999-01-01

    Illustrates an approach to research-based teaching strategies and their evaluation. Addresses a teaching sequence on the superposition of electric fields implemented at the college level in an institutional framework subject to severe constraints. Contains 28 references. (DDR)

  12. Base J glucosyltransferase does not regulate the sequence specificity of J synthesis in trypanosomatid telomeric DNA.

    Science.gov (United States)

    Bullard, Whitney; Cliffe, Laura; Wang, Pengcheng; Wang, Yinsheng; Sabatini, Robert

    2015-12-01

    Telomeric DNA of trypanosomatids possesses a modified thymine base, called base J, that is synthesized in a two-step process; the base is hydroxylated by a thymidine hydroxylase forming hydroxymethyluracil (hmU) and a glucose moiety is then attached by the J-associated glucosyltransferase (JGT). To examine the importance of JGT in modifiying specific thymine in DNA, we used a Leishmania episome system to demonstrate that the telomeric repeat (GGGTTA) stimulates J synthesis in vivo while mutant telomeric sequences (GGGTTT, GGGATT, and GGGAAA) do not. Utilizing an in vitro GT assay we find that JGT can glycosylate hmU within any sequence with no significant change in Km or kcat, even mutant telomeric sequences that are unable to be J-modified in vivo. The data suggests that JGT possesses no DNA sequence specificity in vitro, lending support to the hypothesis that the specificity of base J synthesis is not at the level of the JGT reaction. PMID:26815240

  13. Correlated mutations in protein sequences: Phylogenetic and structural effects

    Energy Technology Data Exchange (ETDEWEB)

    Lapedes, A.S. [Los Alamos National Lab., NM (United States). Theoretical Div.]|[Santa Fe Inst., NM (United States); Giraud, B.G. [C.E.N. Saclay, Gif/Yvette (France). Service Physique Theorique; Liu, L.C. [Los Alamos National Lab., NM (United States). Theoretical Div.; Stormo, G.D. [Univ. of Colorado, Boulder, CO (United States). Dept. of Molecular, Cellular and Developmental Biology

    1998-12-01

    Covariation analysis of sets of aligned sequences for RNA molecules is relatively successful in elucidating RNA secondary structure, as well as some aspects of tertiary structure. Covariation analysis of sets of aligned sequences for protein molecules is successful in certain instances in elucidating certain structural and functional links, but in general, pairs of sites displaying highly covarying mutations in protein sequences do not necessarily correspond to sites that are spatially close in the protein structure. In this paper the authors identify two reasons why naive use of covariation analysis for protein sequences fails to reliably indicate sequence positions that are spatially proximate. The first reason involves the bias introduced in calculation of covariation measures due to the fact that biological sequences are generally related by a non-trivial phylogenetic tree. The authors present a null-model approach to solve this problem. The second reason involves linked chains of covariation which can result in pairs of sites displaying significant covariation even though they are not spatially proximate. They present a maximum entropy solution to this classic problem of causation versus correlation. The methodologies are validated in simulation.

  14. On Properties of Update Sequences Based on Causal Rejection

    OpenAIRE

    Eiter, T.; Fink, M; Sabbatini, G; Tompits, H.

    2001-01-01

    We consider an approach to update nonmonotonic knowledge bases represented as extended logic programs under answer set semantics. New information is incorporated into the current knowledge base subject to a causal rejection principle enforcing that, in case of conflicts, more recent rules are preferred and older rules are overridden. Such a rejection principle is also exploited in other approaches to update logic programs, e.g., in dynamic logic programming by Alferes et al. We give a thoroug...

  15. Team-Based Learning to Improve Learning Outcomes in a Therapeutics Course Sequence

    Science.gov (United States)

    Remington, Tami L.; Wells, Trisha D.; Dorsch, Michael P.; Guthrie, Sally K.; Stumpf, Janice L.; Alaniz, Marissa C.; Ellingrod, Vicki L.; Tingen, Jeffrey M.

    2014-01-01

    Objective. To compare the effectiveness of team-based learning (TBL) to that of traditional lectures on learning outcomes in a therapeutics course sequence. Design. A revised TBL curriculum was implemented in a therapeutic course sequence. Multiple choice and essay questions identical to those used to test third-year students (P3) taught using a traditional lecture format were administered to the second-year pharmacy students (P2) taught using the new TBL format. Assessment. One hundred thirty-one multiple-choice questions were evaluated; 79 tested recall of knowledge and 52 tested higher level, application of knowledge. For the recall questions, students taught through traditional lectures scored significantly higher compared to the TBL students (88%±12% vs 82%±16%, p=0.01). For the questions assessing application of knowledge, no differences were seen between teaching pedagogies (81%±16% vs 77%±20%, p=0.24). Scores on essay questions and the number of students who achieved 100% were also similar between groups. Conclusion. Transition to a TBL format from a traditional lecture-based pedagogy allowed P2 students to perform at a similar level as students with an additional year of pharmacy education on application of knowledge type questions. However, P3 students outperformed P2 students regarding recall type questions and overall. Further assessment of long-term learning outcomes is needed to determine if TBL produces more persistent learning and improved application in clinical settings. PMID:24558281

  16. Sequencing-Based Genotyping of Mixed Human Papillomavirus Infections by Use of RipSeq Software

    OpenAIRE

    Tardif, Keith D.; Simmon, Keith E.; Kommedal, Øyvind; Pyne, Michael T.; Schlaberg, Robert

    2013-01-01

    Sequencing-based pathogen identification directly from clinical specimens requires time-consuming interpretation, especially with mixed chromatograms when multiple microorganisms are detected. We assessed RipSeq Mixed software for human papillomavirus (HPV) genotyping by comparison to the linear array HPV genotyping assay. RipSeq Mixed provided rapid, sequencing-based HPV typing for single-type infections and coinfections with 2 types.

  17. Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns

    OpenAIRE

    Comin, Matteo; Schimd, Michele

    2014-01-01

    Background With the advent of Next-Generation Sequencing technologies (NGS), a large amount of short read data has been generated. If a reference genome is not available, the assembly of a template sequence is usually challenging because of repeats and the short length of reads. When NGS reads cannot be mapped onto a reference genome alignment-based methods are not applicable. However it is still possible to study the evolutionary relationship of unassembled genomes based on NGS data. Results...

  18. Rigorous assessment and integration of the sequence and structure based features to predict hot spots

    Directory of Open Access Journals (Sweden)

    Wang Yong

    2011-07-01

    Full Text Available Abstract Background Systematic mutagenesis studies have shown that only a few interface residues termed hot spots contribute significantly to the binding free energy of protein-protein interactions. Therefore, hot spots prediction becomes increasingly important for well understanding the essence of proteins interactions and helping narrow down the search space for drug design. Currently many computational methods have been developed by proposing different features. However comparative assessment of these features and furthermore effective and accurate methods are still in pressing need. Results In this study, we first comprehensively collect the features to discriminate hot spots and non-hot spots and analyze their distributions. We find that hot spots have lower relASA and larger relative change in ASA, suggesting hot spots tend to be protected from bulk solvent. In addition, hot spots have more contacts including hydrogen bonds, salt bridges, and atomic contacts, which favor complexes formation. Interestingly, we find that conservation score and sequence entropy are not significantly different between hot spots and non-hot spots in Ab+ dataset (all complexes. While in Ab- dataset (antigen-antibody complexes are excluded, there are significant differences in two features between hot pots and non-hot spots. Secondly, we explore the predictive ability for each feature and the combinations of features by support vector machines (SVMs. The results indicate that sequence-based feature outperforms other combinations of features with reasonable accuracy, with a precision of 0.69, a recall of 0.68, an F1 score of 0.68, and an AUC of 0.68 on independent test set. Compared with other machine learning methods and two energy-based approaches, our approach achieves the best performance. Moreover, we demonstrate the applicability of our method to predict hot spots of two protein complexes. Conclusion Experimental results show that support vector machine

  19. Effects of KLK Peptide on Adjuvanticity of Different ODN Sequences.

    Science.gov (United States)

    Chikh, Ghania; Luu, Rachel; Patel, Shobhna; Davis, Heather L; Weeratna, Risini D

    2016-01-01

    Endosomal Toll-like receptors (TLR) such as TLR3, 7, 8 and 9 recognize pathogen associated nucleic acids. While DNA sequence does influence degree of binding to and activation of TLR9, it also appears to influence the ability of the ligand to reach the intracellular endosomal compartment. The KLK (KLKL5KLK) antimicrobial peptide, which is immunostimulatory itself, can translocate into cells without cell membrane permeabilization and thus can be used for endosomal delivery of TLR agonists, as has been shown with the IC31 formulation that contains an oligodeoxynucleotide (ODN) TLR9 agonist. We evaluated the adjuvant activity of KLK combined with CpG or non-CpG (GpC) ODN synthesized with nuclease resistant phosphorothioate (S) or native phosphodiester (O) backbones with ovalbumin (OVA) antigen in mice. As single adjuvants, CpG(S) gave the strongest enhancement of OVA-specific immunity and the addition of KLK provided no benefit and was actually detrimental for some readouts. In contrast, KLK enhanced the adjuvant effects of CpG(O) and to a lesser extent of GpC (S), which on their own had little or no activity. Indeed while CD8 T cells, IFN-γ secretion and humoral response to vaccine antigen were enhanced when CpG(O) was combined with KLK, only IFN-γ secretion was enhanced when GpC (S) was combined to KLK. The synergistic adjuvant effects with KLK/ODN combinations were TLR9-mediated since they did not occur in TLR9 knock-out mice. We hypothesize that a nuclease resistant ODN with CpG motifs has its own mechanism for entering cells to reach the endosome. For ODN without CpG motifs, KLK appears to provide an alternate mechanism for accessing the endosome, where it can activate TLR9, albeit with lower potency than a CpG ODN. For nuclease sensitive (O) backbone ODN, KLK may also provide protection from nucleases in the tissues. PMID:27153098

  20. Effects of KLK Peptide on Adjuvanticity of Different ODN Sequences

    Directory of Open Access Journals (Sweden)

    Ghania Chikh

    2016-05-01

    Full Text Available Endosomal Toll-like receptors (TLR such as TLR3, 7, 8 and 9 recognize pathogen associated nucleic acids. While DNA sequence does influence degree of binding to and activation of TLR9, it also appears to influence the ability of the ligand to reach the intracellular endosomal compartment. The KLK (KLKL5KLK antimicrobial peptide, which is immunostimulatory itself, can translocate into cells without cell membrane permeabilization and thus can be used for endosomal delivery of TLR agonists, as has been shown with the IC31 formulation that contains an oligodeoxynucleotide (ODN TLR9 agonist. We evaluated the adjuvant activity of KLK combined with CpG or non-CpG (GpC ODN synthesized with nuclease resistant phosphorothioate (S or native phosphodiester (O backbones with ovalbumin (OVA antigen in mice. As single adjuvants, CpG(S gave the strongest enhancement of OVA-specific immunity and the addition of KLK provided no benefit and was actually detrimental for some readouts. In contrast, KLK enhanced the adjuvant effects of CpG(O and to a lesser extent of GpC (S, which on their own had little or no activity. Indeed while CD8 T cells, IFN-γ secretion and humoral response to vaccine antigen were enhanced when CpG(O was combined with KLK, only IFN-γ secretion was enhanced when GpC (S was combined to KLK. The synergistic adjuvant effects with KLK/ODN combinations were TLR9-mediated since they did not occur in TLR9 knock-out mice. We hypothesize that a nuclease resistant ODN with CpG motifs has its own mechanism for entering cells to reach the endosome. For ODN without CpG motifs, KLK appears to provide an alternate mechanism for accessing the endosome, where it can activate TLR9, albeit with lower potency than a CpG ODN. For nuclease sensitive (O backbone ODN, KLK may also provide protection from nucleases in the tissues.

  1. Rapid Conversion of Traditional Introductory Physics Sequences to an Activity-Based Format

    Science.gov (United States)

    Yoder, Garett; Cook, Jerry

    2014-01-01

    The Department of Physics at EKU [Eastern Kentucky University] with support from the National Science Foundations Course Curriculum and Laboratory Improvement Program has successfully converted our entire introductory physics sequence, both algebra-based and calculus-based courses, to an activity-based format where laboratory activities,…

  2. Cultural sequence of Bet Dwarka Island based on thermoluminescence dating

    Digital Repository Service at National Institute of Oceanography (India)

    Vora, K.H.; Gaur, A.S.; Price, D.; Sundaresh

    minerals may not store TL in a stable fashion over long time periods. Aitken 14 suggests that the first defence against such an effect is the so - called temperature pla teau comparison, where the shape of the first TL glow - curves are compared...

  3. Sequence effect in Parkinson’s disease is related to motor energetic cost

    OpenAIRE

    Sule eTinaz; Pillai, Ajay S.; Mark eHallett

    2016-01-01

    Bradykinesia is the most disabling motor symptom of Parkinson’s disease (PD). The sequence effect, a feature of bradykinesia, refers to the rapid decrement in amplitude and speed of repetitive movements (e.g., gait, handwriting) and is a major cause of morbidity in PD. Previous research has revealed mixed results regarding the role of dopaminergic treatment in the sequence effect. However, external cueing has been shown to improve it. In this study, we aimed to characterize the sequence effec...

  4. Astrobiology in the Environments of Main-Sequence Stars: Effects of Photospheric Radiation

    OpenAIRE

    Cuntz, M.; Gurdemir, L.; Guinan, E. F.; Kurucz, R. L.

    2007-01-01

    We explore if carbon-based macromolecules (such as DNA) in the environments of stars other than the Sun are able to survive the effects of photospheric stellar radiation, such as UV-C. Therefore, we focus on main-sequence stars of spectral types F, G, K, and M. Emphasis is placed on investigating the radiative environment in the stellar habitable zones. Stellar habitable zones are relevant to astrobiology because they constitute circumstellar regions in which a planet of suitable size can mai...

  5. MRI-Based Thermometry for Tumor Thermal Ablation: A Comparison of Different MR Sequences

    Directory of Open Access Journals (Sweden)

    T. J. Vogl

    2010-05-01

    Full Text Available Background/Objective: To evaluate T1 and PRF thermometry methods utilizing fast MR sequences and fluoroptic thermometer."nMaterials and Methods: The MR-guided LITT (Laser-Induced Interstitial Thermotherapy with a laser wavelength/power of 1064nm/30W was applied to pig liver and a gel phantom. During the ablation process, the temperature was measured using a fluoroptic thermometer and MR imaging was performed applying a 1.5-Tesla tomograph with an EPI (Echo Planar Imaging sequence for PRF (Proton Resonance Frequency method and FLASH, IRTF, SRTF and TRUFI sequences for T1 method. Plotting MR signal intensity against measured temperature determined the temperature constant for each of the T1 sequences. To determine the PRF temperature constant, phase values were recorded from phase images and then plotted against temperature. The PRF temperature constant was verified comparing the MR temperature with the measured one obtained from a second LITT experiment on gel phantom."nResults: The experiments determining the temperature constant for T1 method showed that the IRTF and FLASH sequences have the highest temperature sensitivity and the most linear relationship between MR signal intensity and measured temperature. SRTF sequence presented relatively good linearity but inferior temperature sensitivity compared to IRTF and FLASH sequences. Conversely, TRUFI sequence exhibited the lowest temperature sensitivity and linearity of data points. Concerning the PRF method, the measured and the MR-based temperatures agreed up to approximately 70 C."nConclusion: To demonstrate and control temperature in target tissue during the LITT process, the PRF method with an EPI sequence is preferred for temperatures below 70 C due to its acceptable accuracy. Among the T1 sequences, FLASH is preferable as the most robust, though not the most accurate T1 sequence.

  6. Park-based and zero sequence-based relaying techniques with application to transformers protection

    Energy Technology Data Exchange (ETDEWEB)

    Diaz, G.; Arboleya, P.; Gomez-Aleixandre, J. [University of Oviedo (Spain). Dept. of Electrical Engineering

    2004-09-01

    Two relaying techniques for protecting power transformers are presented and discussed. Very often, differential relaying is used for this purpose. A comparison between the two proposed techniques and conventional differential relaying is thus presented. The first technique, based on the measurements of zero sequence current within a delta winding, performs best in multiwinding transformers, since only measurement of the coil currents is needed. Thus, great simplicity is achieved. The second one is based on the differential procedure, but its analysis of asymmetries in the plot in Park's plane avoids problems related to spectral analysis in conventional differential relaying. The technique is justified from the analysis of symmetrical components. Misoperation in conventional differential relaying has been observed in some cases as a function of switching instant and fault location. This issue is discussed in the paper, and a statistical analysis of a large number of laboratory tests, in which both factors were controlled, is presented. As a conclusion, both relaying techniques proposed succeed in protecting the transformer. Additionally, the Park-based relay exhibits three characteristics of most importance: fastest performance, robustness and simplicity in its formulation. (author)

  7. Diversity Analysis in Cannabis sativa Based on Large-Scale Development of Expressed Sequence Tag-Derived Simple Sequence Repeat Markers

    OpenAIRE

    Gao, Chunsheng; Xin, Pengfei; Cheng, Chaohua; Tang, Qing; Ping CHEN; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

    2014-01-01

    Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SS...

  8. Effects of Early Musical Experience on Auditory Sequence Memory

    Science.gov (United States)

    Tierney, Adam T.; Bergeson-Dana, Tonya R.; Pisoni, David B.

    2009-01-01

    The present study investigated a possible link between musical training and immediate memory span by testing experienced musicians and three groups of musically inexperienced subjects (gymnasts, Psychology 101 students, and video game players) on sequence memory and word familiarity tasks. By including skilled gymnasts who began studying their craft by age six, video game players, and Psychology 101 students as comparison groups, we attempted to control for some of the ways skilled musicians may differ from participants drawn from the general population in terms of gross motor skills and intensive experience in a highly skilled domain from an early age. We found that musicians displayed longer immediate memory spans than the comparison groups on auditory presentation conditions of the sequence reproductive span task. No differences were observed between the four groups on the visual conditions of the sequence memory task. These results provide additional converging support to recent findings showing that early musical experience and activity-dependent learning may selectively affect verbal rehearsal processes and the allocation of attention in sequence memory tasks. PMID:21394231

  9. Reassociation kinetics-based approach for partial genome sequencing of the cattle tick, Rhipicephalus (Boophilus microplus

    Directory of Open Access Journals (Sweden)

    Bellgard Matthew

    2010-06-01

    Full Text Available Abstract Background The size and repetitive nature of the Rhipicephalus microplus genome makes obtaining a full genome sequence fiscally and technically problematic. To selectively obtain gene-enriched regions of this tick's genome, Cot filtration was performed, and Cot-filtered DNA was sequenced via 454 FLX pyrosequencing. Results The sequenced Cot-filtered genomic DNA was assembled with an EST-based gene index of 14,586 unique entries where each EST served as a potential "seed" for scaffold formation. The new sequence assembly extended the lengths of 3,913 of the 14,586 gene index entries. Over half of the extensions corresponded to extensions of over 30 amino acids. To survey the repetitive elements in the tick genome, the complete sequences of five BAC clones were determined. Both Class I and II transposable elements were found. Comparison of the BAC and Cot filtration data indicates that Cot filtration was highly successful in filtering repetitive DNA out of the genomic DNA used in 454 sequencing. Conclusion Cot filtration is a very useful strategy to incorporate into genome sequencing projects on organisms with large genome sizes and which contain high percentages of repetitive, difficult to assemble, genomic DNA. Combining the Cot selection approach with 454 sequencing and assembly with a pre-existing EST database as seeds resulted in extensions of 27% of the members of the EST database.

  10. Performance of Correspondence Algorithms in Vision-Based Driver Assistance Using an Online Image Sequence Database

    DEFF Research Database (Denmark)

    Klette, Reinhard; Krüger, Norbert; Vaudrey, Tobi;

    2011-01-01

    This paper discusses options for testing correspondence algorithms in stereo or motion analysis that are designed or considered for vision-based driver assistance. It introduces a globally available database, with a main focus on testing on video sequences of real-world data. We suggest the......) for demonstrating ideas, difficulties, and possible ways in this future field of extensive performance tests in vision-based driver assistance, particularly for cases where the ground truth is not available. This paper shows that the complexity of real-world data does not support the identification of...... report on hours of driving, and multiple hours of long video data may be segmented into basic sequences and classified into situations. This paper prepares for this expected development. This paper uses three different evaluation approaches (prediction error, synthesized sequences, and labeled sequences...

  11. A 502-Base Free-Solution Electrophoretic DNA Sequencing Method Using End-Attached Wormlike Micelles.

    Science.gov (United States)

    Istivan, Stephen B; Bishop, Daniel K; Jones, Angela L; Grosser, Shane T; Schneider, James W

    2015-11-17

    We demonstrate that the use of wormlike nonionic micelles as drag-tags in end-labeled free-solution electrophoresis ("micelle-ELFSE") provides single-base resolution of Sanger sequencing products up to 502 bases in length, a nearly 2-fold improvement over reported ELFSE separations. "CiEj" running buffers containing 48 mM C12E5, 6 mM C10E5, and 3 M urea (32.5 °C) form wormlike micelles that provide a drag equivalent to an uncharged DNA fragment with a length (α) of 509 bases (effective Rh = 27 nm). Runtime in a 40 cm capillary (30 kV) was 35 min for elution of all products down to the 26-base primer. We also show that smaller Triton X-100 micelles give a read length of 103 bases in a 4 min run, so that a combined analysis of the Sanger products using the two buffers in separate capillaries could be completed in 14 min for the full range of lengths. A van Deemter analysis shows that resolution is limited by diffusion-based peak broadening and wall adsorption. Effects of drag-tag polydispersity are not observed, despite the inherent polydispersity of the wormlike micelles. We ascribe this to a stochastic size-sampling process that occurs as micelle size fluctuates rapidly during the runtime. A theoretical model of the process suggests that fluctuations occur with a time scale less than 10 ms, consistent with the monomer exchange process in nonionic micelles. The CiEj buffer has a low viscosity (2.7 cP) and appears to be semidilute in micelle concentration. The large drag-tag size of the CiEj buffers leads to steric segregation of the DNA and tag for short fragments and attendant mobility shifts. PMID:26455271

  12. Feature Based Image Sequence Retargeting in the Uncompressed Video Domain

    Directory of Open Access Journals (Sweden)

    Kavitha. S

    2013-01-01

    Full Text Available The system propose a video retargeting algorithmto resize images based on the extracted saliency informationfrom the compressed domain. The system utilizes DCTcoefficients in JP2 bit stream to perform saliency detectionwith the consideration of the human visual sensitivity.Valuable retargeting requires emphasize the main satisfiedwhile retain immediate context with minimal visualdeformation. A number of algorithms have been proposedfor image retargeting with image substance taken as muchas potential. But, they usually suffer from deformationresults, such as edge or structure twists. A structure andcontent preserving image retargeting technique is used thatpreserves the content and image structure. The imagecontent saliency is estimated from the structure of thecontent using probability map. A block structure energy isuse for structure conservation along both directions. Blockstructure energy uses top down strategy to constrict theimage structure consistently. However, the flexibilities ofretargeting are altered for different images. To defeat thisproblem, the patch transform is introduced, where an imageis broken into non-overlapping patches, and modificationsor constraints are applied in the “patch domain”.. Thus, theresized image is produced to preserve the structure andimage content quality.

  13. Statistical framework for detection of genetically modified organisms based on Next Generation Sequencing

    OpenAIRE

    Willems, Sander; Fraiture, Marie-Alice; Deforce, Dieter; De Keersmaecker, Sigrid; Herman, Philippe; De Loose, Marc; Ruttink, Tom; Van Nieuwerburgh, Filip; Roosens, Nancy

    2016-01-01

    Because the number and diversity of genetically modified (GM) crops has significantly increased, their analysis based on real-time PCR (qPCR) methods is becoming increasingly complex and laborious. While several pioneers already investigated Next Generation Sequencing (NGS) as an alternative to qPCR, its practical use has not been assessed for routine analysis. In this study a statistical framework was developed to predict the number of NGS reads needed to detect transgene sequences, to prove...

  14. Switching Loss Characteristics of Sequences Involving Active State Division in Space Vector Based PWM

    OpenAIRE

    Zhao, Di; Narayanan, G.; Ayyanar, Raja

    2004-01-01

    This paper analyzes the switching loss characteristics of sequences involving division of active state duration in space vector based PWM. This analysis, together with the THD performance of the different sequences, reported recently, is used to design new hybrid PWM techniques for induction motor drives, which result in simultaneous reduction in both THD as well as inverter switching losses. Experimental results are presented to demonstrate the feasibility and advantages of the proposed PWM ...

  15. PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

    OpenAIRE

    Francisco Alexandre P; Vaz Ctia; Monteiro Pedro T; Melo-Cristino José; Ramirez Mário; Carrio Joo A

    2012-01-01

    Abstract Background With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains under...

  16. CloudMap: A Cloud-Based Pipeline for Analysis of Mutant Genome Sequences

    OpenAIRE

    Minevich, Gregory; Park, Danny S.; Blankenberg, Daniel; Richard J Poole; Hobert, Oliver

    2012-01-01

    Whole genome sequencing (WGS) allows researchers to pinpoint genetic differences between individuals and significantly shortcuts the costly and time-consuming part of forward genetic analysis in model organism systems. Currently, the most effort-intensive part of WGS is the bioinformatic analysis of the relatively short reads generated by second generation sequencing platforms. We describe here a novel, easily accessible and cloud-based pipeline, called CloudMap, which greatly simplifies the ...

  17. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.

    Directory of Open Access Journals (Sweden)

    Brejnev Muhizi Muhire

    Full Text Available The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV. There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT, a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms.

  18. Effects of early musical experience on auditory sequence memory

    OpenAIRE

    Tierney, Adam T.; Bergeson-Dana, Tonya R.; Pisoni, David B.

    2008-01-01

    The present study investigated a possible link between musical training and immediate memory span by testing experienced musicians and three groups of musically inexperienced subjects (gymnasts, Psychology 101 students, and video game players) on sequence memory and word familiarity tasks. By including skilled gymnasts who began studying their craft by age six, video game players, and Psychology 101 students as comparison groups, we attempted to control for some of the ways skilled musicians ...

  19. EFFECT OF DYE CONCENTRATION ON SEQUENCING BATCH REACTOR PERFORMANCE

    OpenAIRE

    A. A. Vaigan ، M. R. Alavi Moghaddam ، H. Hashemi

    2009-01-01

    Reactive dyes have been identified as problematic compounds in textile industries wastewater as they are water soluble and cannot be easily removed by conventional aerobic biological treatment systems. The treatability of a reactive dye (Brill Blue KN-R) by sequencing batch reactor and the influence of the dye concentration on system performance were investigated in this study. Brill Blue KN-R is one of the main dyes that are used in textile industries in Iran. Four cylindrical Plexiglas reac...

  20. Quasi-Coherent Noise Jamming to LFM Radar Based on Pseudo-random Sequence Phase-modulation

    OpenAIRE

    Tai, N.; Pan, Y. J.; Yuan, N. C.

    2015-01-01

    A novel quasi-coherent noise jamming method is proposed against linear frequency modulation (LFM) signal and pulse compression radar. Based on the structure of digital radio frequency memory (DRFM), the jamming signal is acquired by the pseudo-random sequence phase-modulation of sampled radar signal. The characteristic of jamming signal in time domain and frequency domain is analyzed in detail. Results of ambiguity function indicate that the blanket jamming effect along the range direction wi...

  1. Capturing Human Motion based on Modified Hidden Markov Model in Multi-View Image Sequences

    Directory of Open Access Journals (Sweden)

    Yanan Liu

    2014-01-01

    Full Text Available Human motion capturing is of great importance in video information retrieval, hence, in this paper, we propose a novel approach to effectively capturing human motions based on modified hidden markov model from multi-view image sequences. Firstly, the structure of the human skeleton model is illustrated, which is extended from skeleton root and spine root, and this skeleton consists of right leg, left leg and spine. Secondly, our proposed human motion capturing system is made up of data training module and human motion capturing module. In the data training module, multi-views motion information is extracted from a human motion database, and feature database of human motion capturing is constructed through combining multi-views motions. In the human motion capturing module, results of motion capturing can be achieved through motion classification based on a modified hidden markov model. Thirdly, the modified hidden markov model is designed by utilizing the fuzzy measure, fuzzy integer, and fuzzy intersection operator through a scaling process. Finally, a standard motion capture dataset- MPI08_Database is utilized to make performance evaluation. Compared with the existing methods, the proposed approach can effectively capture human motions with high precision

  2. High Throughput Sample Preparation and Analysis for DNA Sequencing, PCR and Combinatorial Screening of Catalysis Based on Capillary Array Technique

    Energy Technology Data Exchange (ETDEWEB)

    Yonghua Zhang

    2002-05-27

    Sample preparation has been one of the major bottlenecks for many high throughput analyses. The purpose of this research was to develop new sample preparation and integration approach for DNA sequencing, PCR based DNA analysis and combinatorial screening of homogeneous catalysis based on multiplexed capillary electrophoresis with laser induced fluorescence or imaging UV absorption detection. The author first introduced a method to integrate the front-end tasks to DNA capillary-array sequencers. protocols for directly sequencing the plasmids from a single bacterial colony in fused-silica capillaries were developed. After the colony was picked, lysis was accomplished in situ in the plastic sample tube using either a thermocycler or heating block. Upon heating, the plasmids were released while chromsomal DNA and membrane proteins were denatured and precipitated to the bottom of the tube. After adding enzyme and Sanger reagents, the resulting solution was aspirated into the reaction capillaries by a syringe pump, and cycle sequencing was initiated. No deleterious effect upon the reaction efficiency, the on-line purification system, or the capillary electrophoresis separation was observed, even though the crude lysate was used as the template. Multiplexed on-line DNA sequencing data from 8 parallel channels allowed base calling up to 620 bp with an accuracy of 98%. The entire system can be automatically regenerated for repeated operation. For PCR based DNA analysis, they demonstrated that capillary electrophoresis with UV detection can be used for DNA analysis starting from clinical sample without purification. After PCR reaction using cheek cell, blood or HIV-1 gag DNA, the reaction mixtures was injected into the capillary either on-line or off-line by base stacking. The protocol was also applied to capillary array electrophoresis. The use of cheaper detection, and the elimination of purification of DNA sample before or after PCR reaction, will make this approach an

  3. Sequence and solvent effects on telomeric DNA bimolecular G-quadruplex folding kinetics.

    Science.gov (United States)

    Marchand, Adrien; Ferreira, Rubén; Tateishi-Karimata, Hisae; Miyoshi, Daisuke; Sugimoto, Naoki; Gabelica, Valérie

    2013-10-17

    Telomeric DNA sequences are particularly polymorphic: the adopted structure is exquisitely sensitive to the sequence and to the chemical environment, for example, solvation. Dehydrating conditions are known to stabilize G-quadruplex structures, but information on how solvation influences the individual rates of folding and unfolding of G-quadruplexes remains scarce. Here, we used electrospray mass spectrometry for the first time to monitor bimolecular G-quadruplex formation from 12-mer telomeric strands, in the presence of common organic cosolvents (methanol, ethanol, isopropanol, and acetonitrile). Based on the ammonium ion distribution, the total dimer signal was decomposed into contributions from the parallel and antiparallel structures to obtain individual reaction rates, and the antiparallel G-quadruplex structure was found to form faster than the parallel one. A dimeric reaction intermediate, in rapid equilibrium with the single strands, was also identified. Organic cosolvents increase the stability of the final structures mainly by increasing the folding rates. Our quantitative analysis of reaction rate dependence on cosolvent percentage shows that organic cosolvent molecules can be captured or released upon G-quadruplex formation, highlighting that they are not inert with DNA. In contrast to the folding rates, the G-quadruplex unfolding rates are almost insensitive to solvation effects, but are instead governed by the sequence and by the final structure: parallel dimers dissociate slower than antiparallel dimers only when thymine bases are present at the 5'-end. These results contribute unraveling the folding pathways of telomeric G-quadruplexes. The solvent effects revealed here enlighten that G-quadruplex structure in dehydrated, and molecularly crowded environments are modulated by the nature of cosolvent (e.g., methanol favors antiparallel structures) due to direct interactions, and by the time scale of the reaction, with >200-fold acceleration of

  4. Construction of a phylogenetic tree of photosynthetic prokaryotes based on average similarities of whole genome sequences.

    Directory of Open Access Journals (Sweden)

    Soichirou Satoh

    Full Text Available Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.

  5. Quasi-Coherent Noise Jamming to LFM Radar Based on Pseudo-random Sequence Phase-modulation

    Directory of Open Access Journals (Sweden)

    N. Tai

    2015-12-01

    Full Text Available A novel quasi-coherent noise jamming method is proposed against linear frequency modulation (LFM signal and pulse compression radar. Based on the structure of digital radio frequency memory (DRFM, the jamming signal is acquired by the pseudo-random sequence phase-modulation of sampled radar signal. The characteristic of jamming signal in time domain and frequency domain is analyzed in detail. Results of ambiguity function indicate that the blanket jamming effect along the range direction will be formed when jamming signal passes through the matched filter. By flexible controlling the parameters of interrupted-sampling pulse and pseudo-random sequence, different covering distances and jamming effects will be achieved. When the jamming power is equivalent, this jamming obtains higher process gain compared with non-coherent jamming. The jamming signal enhances the detection threshold and the real target avoids being detected. Simulation results and circuit engineering implementation validate that the jamming signal covers real target effectively.

  6. An Optimal Sorting of Pulse Amplitude Sequence Based on the Phased Array Radar Beam Tasks

    Institute of Scientific and Technical Information of China (English)

    Chuan Sheng∗,Yongshun Zhang; Wenlong Lu

    2016-01-01

    The study of phased array radar ( PAR) pulse amplitude sequence characteristics is the key to understand the radar’s working state and its beam’s scanning manner. According to the principle of antenna pattern formation and the searching and tracking modes of beams, this paper analyzes the characteristics and differences of pulse amplitude sequence when the radar beams work in searching and tracking modes respectively. Then an optimal sorting model of pulse amplitude sequence is established based on least⁃squares and curve⁃fitting methods. This method is helpful for acquiring the current working state of the radar and recognizing its instantaneous beam pointing by sorting the pulse amplitude sequence without the necessity to estimate the antenna pattern.

  7. Fast interactive segmentation algorithm of image sequences based on relative fuzzy connectedness

    Institute of Scientific and Technical Information of China (English)

    Tian Chunna; Gao Xinbo

    2005-01-01

    A fast interactive segmentation algorithm of image-sequences based on relative fuzzy connectedness is presented. In comparison with the original algorithm, the proposed one, with the same accuracy, accelerates the segmentation speed by three times for single image. Meanwhile, this fast segmentation algorithm is extended from single object to multiple objects and from single-image to image-sequences. Thus the segmentation of multiple objects from complex background and batch segmentation of image-sequences can be achieved. In addition, a post-processing scheme is incorporated in this algorithm, which extracts smooth edge with one-pixel-width for each segmented object. The experimental results illustrate that the proposed algorithm can obtain the object regions of interest from medical image or image-sequences as well as man-made images quickly and reliably with only a little interaction.

  8. Weather data analysis based on typical weather sequence analysis. Application: energy building simulation

    CERN Document Server

    David, Mathieu; Garde, Francois; Boyer, Harry

    2014-01-01

    In building studies dealing about energy efficiency and comfort, simulation software need relevant weather files with optimal time steps. Few tools generate extreme and mean values of simultaneous hourly data including correlation between the climatic parameters. This paper presents the C++ Runeole software based on typical weather sequences analysis. It runs an analysis process of a stochastic continuous multivariable phenomenon with frequencies properties applied to a climatic database. The database analysis associates basic statistics, PCA (Principal Component Analysis) and automatic classifications. Different ways of applying these methods will be presented. All the results are stored in the Runeole internal database that allows an easy selection of weather sequences. The extreme sequences are used for system and building sizing and the mean sequences are used for the determination of the annual cooling loads as proposed by Audrier-Cros (Audrier-Cros, 1984). This weather analysis was tested with the datab...

  9. Enhancing Students Motivation towards School Science with an Inquiry - Based Site Visit Teaching Sequence: A Design - Based Research Approach

    OpenAIRE

    Anni Loukomies

    2013-01-01

    An inquiry-based site visit teaching sequence for school science was designed in co-operation with researchers and science teachers, according to the principles of Design Based Research (DBR). Out-of-school industry site visits were central in the design. Theory-based conjectures arising from the literature on motivation, interest and inquiry-based science teaching (IBST) were embodied in the design solution, and these embodied conjectures were studied in order to uncover the aspects of the d...

  10. Prediction of Antimicrobial Peptides Based on Sequence Alignment and Support Vector Machine-Pairwise Algorithm Utilizing LZ-Complexity

    Directory of Open Access Journals (Sweden)

    Xin Yi Ng

    2015-01-01

    Full Text Available This study concerns an attempt to establish a new method for predicting antimicrobial peptides (AMPs which are important to the immune system. Recently, researchers are interested in designing alternative drugs based on AMPs because they have found that a large number of bacterial strains have become resistant to available antibiotics. However, researchers have encountered obstacles in the AMPs designing process as experiments to extract AMPs from protein sequences are costly and require a long set-up time. Therefore, a computational tool for AMPs prediction is needed to resolve this problem. In this study, an integrated algorithm is newly introduced to predict AMPs by integrating sequence alignment and support vector machine- (SVM- LZ complexity pairwise algorithm. It was observed that, when all sequences in the training set are used, the sensitivity of the proposed algorithm is 95.28% in jackknife test and 87.59% in independent test, while the sensitivity obtained for jackknife test and independent test is 88.74% and 78.70%, respectively, when only the sequences that has less than 70% similarity are used. Applying the proposed algorithm may allow researchers to effectively predict AMPs from unknown protein peptide sequences with higher sensitivity.

  11. Plasmid-Based Materials as Multiplex Quality Controls and Calibrators for Clinical Next-Generation Sequencing Assays.

    Science.gov (United States)

    Sims, David J; Harrington, Robin D; Polley, Eric C; Forbes, Thomas D; Mehaffey, Michele G; McGregor, Paul M; Camalier, Corinne E; Harper, Kneshay N; Bouk, Courtney H; Das, Biswajit; Conley, Barbara A; Doroshow, James H; Williams, P Mickey; Lih, Chih-Jian

    2016-05-01

    Although next-generation sequencing technologies have been widely adapted for clinical diagnostic applications, an urgent need exists for multianalyte calibrator materials and controls to evaluate the performance of these assays. Control materials will also play a major role in the assessment, development, and selection of appropriate alignment and variant calling pipelines. We report an approach to provide effective multianalyte controls for next-generation sequencing assays, referred to as the control plasmid spiked-in genome (CPSG). Control plasmids that contain approximately 1000 bases of human genomic sequence with a specific mutation of interest positioned near the middle of the insert and a nearby 6-bp molecular barcode were synthesized, linearized, quantitated, and spiked into genomic DNA derived from formalin-fixed, paraffin-embedded-prepared hapmap cell lines at defined copy number ratios. Serial titration experiments demonstrated the CPSGs performed with similar efficiency of variant detection as formalin-fixed, paraffin-embedded cell line genomic DNA. Repetitive analyses of one lot of CPSGs 90 times during 18 months revealed that the reagents were stable with consistent detection of each of the plasmids at similar variant allele frequencies. CPSGs are designed to work across most next-generation sequencing methods, platforms, and data analysis pipelines. CPSGs are robust controls and can be used to evaluate the performance of different next-generation sequencing diagnostic assays, assess data analysis pipelines, and ensure robust assay performance metrics. PMID:27105923

  12. Temporal Extension to Exemplar-based Inpainting Applied to Scratch Correction in Damaged Image Sequences

    Czech Academy of Sciences Publication Activity Database

    Forbin, G.; Besserer, B.; Boldyš, Jiří; Tschumperlé, D.

    Anaheim: ACTA Press, 2005, s. 1-5. ISBN 0-88986-528-0. [Visualization, Imaging, and Image Processing (VIIP 2005). Benidorm (ES), 07.09.2005-09.09.2005] R&D Projects: GA MŠk 1M0572 Institutional research plan: CEZ:AV0Z10750506 Keywords : image sequences * digital restoration * exemplar-based inpainting method Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2009/ZOI/boldys-temporal extension to exemplar-based inpainting applied to scratch correction in damaged image sequences.pdf

  13. Comparison of the effects of the CHESS sequence and the SPAIR sequence for fat saturation

    Science.gov (United States)

    Dong, Kyung-Rae; Goo, Eun-Hoe; Kweon, Dae-Cheol; Chung, Woon-Kwan; Lee, Jong-Woong

    2013-06-01

    This study compared the abilities of the chemical-shift selective saturation(CHESS) and the spectrally-adiabatic inversion recovery (SPAIR) fat-saturation techniques to resolve the recent problems in fat saturation caused by areas of changing volume such as the head and the neck and by metal artifacts when T1 fat-saturation techniques representing the anatomical images and T2 fat-saturation techniques representing pathological images are used. To compare the abilities of CHESS and SPAIR, we acquired images of the head and the neck and of the pelvis, and we compared the contrast-to-noise ratios (CNRs) and the signal-to-noise ratios (SNRs) of the signals from the flexed body parts. Images were taken of the abdomens, heads and necks, and pelvises of 15 men and 15 women (30 in total). In all scanning techniques, the SNRs and the CNRs were calculated based on a quantitative analysis method with a view to obtaining uniform data. According to the study results, the CNRs of the SPAIR and the CHESS techniques for the pelvis in the T1-weighted image were 55.10 and 67.23, respectively. The SNRs of the SPAIR technique were70.61 for muscle and 15.50 for fat whereas the SNRs of the CHESS technique were 79.23 for muscle and 12.00 for fat. For the pelvis in the T2-weighted image, the CNRs of the SPAIR and the CHESS technique were 12.50 and 16.66, respectively. The SNRs of the SPAIR technique were 16.98 for muscle and 5.14 for fat. In contrast, the SNRs of the CHESS technique were 27.90 for muscle and 11.23 for fat. Consequently, the signal intensity was higher in the CHESS than in the SPAIR technique. Nevertheless, with regard to the clinical usefulness, the image quality was higher in the SPAIR technique than in the CHESS technique.

  14. A Model for Protein Sequence Evolution Based on Selective Pressure for Protein Stability: Application to Hemoglobins

    OpenAIRE

    Lorraine Marsh

    2009-01-01

    Negative selection against protein instability is a central influence on evolution of proteins. Protein stability is maintained over evolution despite changes in underlying sequences. An empirical all-site stability-based model of evolution was developed to focus on the selection of residues arising from their contributions to protein stability. In this model, site rates could vary. A structure-based method was used to predict stationary frequencies of hemoglobin residues based on their prope...

  15. Property-based sequence representations do not adequately encode local protein folding information.

    Science.gov (United States)

    Solis, A D; Rackovsky, S

    2007-06-01

    We examine the informatic characteristics of amino acid representations based on physical properties. We demonstrate that sequences rewritten using contracted alphabets based on physical properties do not encode local folding information well. The best four-character alphabet can only encode approximately 57% of the maximum possible amount of structural information. This result suggests that property-based representations that operate on a local length scale are not likely to be useful in homology searches and fold-recognition exercises. PMID:17387739

  16. Local Sequence Information-based Support Vector Machine to Classify Voltage-gated Potassium Channels

    Institute of Scientific and Technical Information of China (English)

    Li-Xia LIU; Meng-Long LI; Fu-Yuan TAN; Min-Chun LU; Ke-Long WANG; Yan-Zhi GUO; Zhi-Ning WEN; Lin JIANG

    2006-01-01

    In our previous work, we developed a computational tool, PreK-ClassK-ClassKv, to predict and classify potassium (K+) channels. For K+ channel prediction (PreK) and classification at family level (ClassK), this method performs well. However, it does not perform so well in classifying voltage-gated potassium (Kv) channels (ClassKv). In this paper, a new method based on the local sequence information of Kv channels is introduced to classify Kv channels. Six transmembrane domains of a Kv channel protein are used to define a protein, and the dipeptide composition technique is used to transform an amino acid sequence to a numerical sequence. A Kv channel protein is represented by a vector with 2000 elements, and a support vector machine algorithm is applied to classify Kv channels. This method shows good performance with averages of total accuracy (Acc), sensitivity (SE), specificity (SP); reliability (R) and Matthews correlation coefficient (MCC) of 98.0%, 89.9%, 100%, 0.95 and 0.94 respectively. The results indicate that the local sequence information-based method is better than the global sequence information-based method to classify Kv channels.

  17. A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples

    Science.gov (United States)

    Wu, Yu-Wei; Ye, Yuzhen

    Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. Among the computational tools recently developed for metagenomic sequence analysis, binning tools attempt to classify all (or most) of the sequences in a metagenomic dataset into different bins (i.e., species), based on various DNA composition patterns (e.g., the tetramer frequencies) of various genomes. Composition-based binning methods, however, cannot be used to classify very short fragments, because of the substantial variation of DNA composition patterns within a single genome. We developed a novel approach (AbundanceBin) for metagenomics binning by utilizing the different abundances of species living in the same environment. AbundanceBin is an application of the Lander-Waterman model to metagenomics, which is based on the l-tuple content of the reads. AbundanceBin achieved accurate, unsupervised, clustering of metagenomic sequences into different bins, such that the reads classified in a bin belong to species of identical or very similar abundances in the sample. In addition, AbundanceBin gave accurate estimations of species abundances, as well as their genome sizes - two important parameters for characterizing a microbial community. We also show that AbundanceBin performed well when the sequence lengths are very short (e.g. 75 bp) or have sequencing errors.

  18. DNA Sequence Optimization Based on Continuous Particle Swarm Optimization for Reliable DNA Computing and DNA Nanotechnology

    Directory of Open Access Journals (Sweden)

    N. K. Khalid

    2008-01-01

    Full Text Available Problem statement: In DNA based computation and DNA nanotechnology, the design of good DNA sequences has turned out to be an essential problem and one of the most practical and important research topics. Basically, the DNA sequence design problem is a multi-objective problem and it can be evaluated using four objective functions, namely, Hmeasure, similarity, continuity and hairpin. Approach: There are several ways to solve multi-objective problem, however, in order to evaluate the correctness of PSO algorithm in DNA sequence design, this problem is converted into single objective problem. Particle Swarm Optimization (PSO is proposed to minimize the objective in the problem, subjected to two constraints: melting temperature and GCcontent. A model is developed to present the DNA sequence design based on PSO computation. Results: Based on experiments and researches done, 20 particles are used in the implementation of the optimization process, where the average values and the standard deviation for 100 runs are shown along with comparison to other existing methods. Conclusion: The results achieve verified that PSO can suitably solves the DNA sequence design problem using the proposed method and model, comparatively better than other approaches.

  19. Radio frequency interference effect on PN code sequence lock detector

    Science.gov (United States)

    Kwon, Hyuck M.; Tu, Kwei; Loh, Y. C.

    1991-01-01

    The authors find the probabilities of detection and false alarm of the pseudonoise (PN) sequence code lock detector when strong radio frequency interference (RFI) hits the communications link. Both a linear model and a soft-limiter nonlinear model for a transponder receiver are considered. In addition, both continuous wave (CW) RFI and pulse RFI are analyzed, and a discussion is included of how strong CW RFI can knock out the PN code lock detector in a linear or a soft-limiter transponder. As an example, the Space Station Freedom forward S-band PN system is evaluated. It is shown that a soft-limiter transponder can protect the PN code lock detector against a typical pulse RFI, but it can degrade the PN code lock detector performance more than a linear transponder if CW RFI hits the link.

  20. Mitochondrial DNA sequence-based phylogenetic relationship among flesh flies of the genus Sarcophaga (Sarcophagidae: Diptera)

    Indian Academy of Sciences (India)

    Neelam Bajpai; Raghav Ram Tewari

    2010-04-01

    The phylogenetic relationships among flesh flies of the family Sarcophagidae has been based mainly on the morphology of male genitalia. However, the male genitalic character-based relationships are far from satisfactory. Therefore, in the present study mitochondrial DNA has been used as marker to unravel genetic relatedness and to construct phylogeny among five sympatric species of the genus Sarcophaga. Two mitochondrial genes viz., cytochrome oxidase subunit 1 (COI) and NAD dehydrogenase subunit 5 (ND5) were sequenced and genetic distance values were calculated on the basis of sequence differences in both the mitochondrial genes. The data revealed very few genetic difference among the five species for the COI and ND5 gene sequences.

  1. Multi-modulus algorithm based on global artificial fish swarm intelligent optimization of DNA encoding sequences.

    Science.gov (United States)

    Guo, Y C; Wang, H; Wu, H P; Zhang, M Q

    2015-01-01

    Aimed to address the defects of the large mean square error (MSE), and the slow convergence speed in equalizing the multi-modulus signals of the constant modulus algorithm (CMA), a multi-modulus algorithm (MMA) based on global artificial fish swarm (GAFS) intelligent optimization of DNA encoding sequences (GAFS-DNA-MMA) was proposed. To improve the convergence rate and reduce the MSE, this proposed algorithm adopted an encoding method based on DNA nucleotide chains to provide a possible solution to the problem. Furthermore, the GAFS algorithm, with its fast convergence and global search ability, was used to find the best sequence. The real and imaginary parts of the initial optimal weight vector of MMA were obtained through DNA coding of the best sequence. The simulation results show that the proposed algorithm has a faster convergence speed and smaller MSE in comparison with the CMA, the MMA, and the AFS-DNA-MMA. PMID:26782395

  2. Taxonomy and phylogeny of the genus citrus based on the nuclear ribosomal dna its region sequence

    International Nuclear Information System (INIS)

    The genus Citrus (Aurantioideae, Rutaceae) is the sole source of the citrus fruits of commerce showing high economic values. In this study, the taxonomy and phylogeny of Citrus species is evaluated using sequence analysis of the ITS region of nrDNA. This study is based on 26 plants materials belonging to 22 Citrus species having wild, domesticated, and cultivated species. Through DNA alignment of the ITS sequence, ITS1 and ITS2 regions showed relatively high variations of sequence length and nucleotide among these Citrus species. According to previous six-tribe discrimination theory by Swingle and Reece, the grouping in our ITS phylogenetic tree reconstructed by ITS sequences was not related to tribe discrimination but species discrimination. However, the molecular analysis could provide more information on citrus taxonomy. Combined with ITS sequences of other subgenera in then true citrus fruit tree group, the ITS phylogenetic tree indicated subgenera Citrus was monophyletic and nearer to Fortunella, Poncirus, and Clymenia compared to Microcitrus and Eremocitrus. Abundant sequence variations of the ITS region shown in this study would help species identification and tribe differentiation of the genus Citrus. (author)

  3. Wavelet-based multifractal analysis of DNA sequences by using chaos-game representation

    International Nuclear Information System (INIS)

    Chaos game representation (CGR) is proposed as a scale-independent representation for DNA sequences and provides information about the statistical distribution of oligonucleotides in a DNA sequence. CGR images of DNA sequences represent some kinds of fractal patterns, but the common multifractal analysis based on the box counting method cannot deal with CGR images perfectly. Here, the wavelet transform modulus maxima (WTMM) method is applied to the multifractal analysis of CGR images. The results show that the scale-invariance range of CGR edge images can be extended to three orders of magnitude, and complete singularity spectra can be calculated. Spectrum parameters such as the singularity spectrum span are extracted to describe the statistical character of DNA sequences. Compared with the singularity spectrum span, exon sequences with a minimal spectrum span have the most uniform fractal structure. Also, the singularity spectrum parameters are related to oligonucleotide length, sequence component and species, thereby providing a method of studying the length polymorphism of repeat oligonucleotides. (general)

  4. DNA LOSSLESS DIFFERENTIAL COMPRESSION ALGORITHM BASED ON SIMILARITY OF GENOMIC SEQUENCE DATABASE

    Directory of Open Access Journals (Sweden)

    Heba Afify

    2011-09-01

    Full Text Available Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need forefficient algorithms for sequence compression and analysis. Data compression and the associatedtechniques coming from information theory are often perceived as being of interest for datacommunication and storage. In recent years, a substantial effort has been made for the application oftextual data compression techniques to various computational biology tasks, ranging from storage andindexing of large datasets to comparison of genomic databases. This paper presents a differentialcompression algorithm that is based on production of difference sequences according to op-code table inorder to optimize the compression of homologous sequences in dataset. Therefore, the stored data arecomposed of reference sequence, the set of differences, and differences locations, instead of storing eachsequence individually. This algorithm does not require a priori knowledge about the statistics of thesequence set. The algorithm was applied to three different datasets of genomic sequences, it achieved upto 195-fold compression rate corresponding to 99.4% space saving.

  5. Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency

    Directory of Open Access Journals (Sweden)

    Inês Soares

    2012-01-01

    Full Text Available The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions. In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L—L-words—in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

  6. Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping.

    Science.gov (United States)

    Milius, Robert P; Heuer, Michael; Valiga, Daniel; Doroschak, Kathryn J; Kennedy, Caleb J; Bolon, Yung-Tsi; Schneider, Joel; Pollack, Jane; Kim, Hwa Ran; Cereb, Nezih; Hollenbach, Jill A; Mack, Steven J; Maiers, Martin

    2015-12-01

    We present an electronic format for exchanging data for HLA and KIR genotyping with extensions for next-generation sequencing (NGS). This format addresses NGS data exchange by refining the Histoimmunogenetics Markup Language (HML) to conform to the proposed Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines (miring.immunogenomics.org). Our refinements of HML include two major additions. First, NGS is supported by new XML structures to capture additional NGS data and metadata required to produce a genotyping result, including analysis-dependent (dynamic) and method-dependent (static) components. A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced. Second, genotype ambiguity is fully represented by integrating Genotype List Strings, which use a hierarchical set of delimiters to represent allele and genotype ambiguity in a complete and accurate fashion. HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and Sequence Based Typing (SBT)), adding features such as allowing multiple group-specific sequencing primers, and fully leveraging techniques that combine multiple methods to obtain a single result, such as SBT integrated with NGS. PMID:26319908

  7. Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.

    Directory of Open Access Journals (Sweden)

    Takeru Nakazato

    Full Text Available High-throughput sequencing technology, also called next-generation sequencing (NGS, has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA. As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called "Gendoo". We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called "DBCLS SRA" (http://sra.dbcls.jp/. This service will improve accessibility to high-quality data from SRA.

  8. Going, going, gone? Proactive control prevents the congruency sequence effect from rapid decay.

    Science.gov (United States)

    Duthoo, W; Abrahamse, E L; Braem, S; Notebaert, W

    2014-07-01

    The congruency sequence effect, the finding of a reduced congruency effect following incongruent trials in conflict tasks, has received considerable attention in the research on cognitive control over the last two decades. This effect can reflect either the expectancy-guided, preparatory biasing of attention in anticipation of the upcoming stimulus (i.e. proactive control), or the phasic enhancement of the attentional set in response to conflict on the previous trial (i.e. reactive control). A recent study by Egner et al. in Front Psychol 1 (2010) set out to contrast these two alternatives, by exploring the congruency sequence effect across a wide range of inter-trial intervals. It was found that congruency sequence effects were subject to rapid decay over time. This decay fits well with the notion of reactive control, while at the same time speaking against the involvement of proactive regulation—which should also (and even mainly) be evident at longer intervals. In the present study, we first replicate the reduction of the congruency sequence effect with increasing inter-trial interval in a face-word Stroop task. In a second experiment, we show that congruency sequence effects are observed at longer intervals, too, when the proportion of trials with the longest inter-trial interval is increased. Our findings indicate that proactive control can prevent the congruency sequence effect from decaying rapidly. PMID:24077774

  9. Modeling compositional dynamics based on GC and purine contents of protein-coding sequences

    Directory of Open Access Journals (Sweden)

    Yu Jun

    2010-11-01

    Full Text Available Abstract Background Understanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge. Results To model the compositional dynamics of protein-coding sequences, we propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, with no prerequisite of homologous sequences or their alignments. We evaluated the two models by quantifying theoretical compositions of a large collection of protein-coding sequences (including 46 of Archaea, 686 of Bacteria, and 826 of Eukarya, yielding consistent theoretical compositions across all the collected sequences. Conclusions We show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms. Reviewers This article was reviewed by Zhaolei Zhang (nominated by Mark Gerstein, Guruprasad Ananda (nominated by Kateryna Makova, and Daniel Haft.

  10. Modeling compositional dynamics based on GC and purine contents of protein-coding sequences

    KAUST Repository

    Zhang, Zhang

    2010-11-08

    Background: Understanding the compositional dynamics of genomes and their coding sequences is of great significance in gaining clues into molecular evolution and a large number of publically-available genome sequences have allowed us to quantitatively predict deviations of empirical data from their theoretical counterparts. However, the quantification of theoretical compositional variations for a wide diversity of genomes remains a major challenge.Results: To model the compositional dynamics of protein-coding sequences, we propose two simple models that take into account both mutation and selection effects, which act differently at the three codon positions, and use both GC and purine contents as compositional parameters. The two models concern the theoretical composition of nucleotides, codons, and amino acids, with no prerequisite of homologous sequences or their alignments. We evaluated the two models by quantifying theoretical compositions of a large collection of protein-coding sequences (including 46 of Archaea, 686 of Bacteria, and 826 of Eukarya), yielding consistent theoretical compositions across all the collected sequences.Conclusions: We show that the compositions of nucleotides, codons, and amino acids are largely determined by both GC and purine contents and suggest that deviations of the observed from the expected compositions may reflect compositional signatures that arise from a complex interplay between mutation and selection via DNA replication and repair mechanisms.Reviewers: This article was reviewed by Zhaolei Zhang (nominated by Mark Gerstein), Guruprasad Ananda (nominated by Kateryna Makova), and Daniel Haft. 2010 Zhang and Yu; licensee BioMed Central Ltd.

  11. Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome.

    Science.gov (United States)

    Singh, Vinod Kumar; Krishnamachari, Annangarachari

    2016-09-01

    Genome-wide experimental studies in Saccharomyces cerevisiae reveal that autonomous replicating sequence (ARS) requires an essential consensus sequence (ACS) for replication activity. Computational studies identified thousands of ACS like patterns in the genome. However, only a few hundreds of these sites act as replicating sites and the rest are considered as dormant or evolving sites. In a bid to understand the sequence makeup of replication sites, a content and context-based analysis was performed on a set of replicating ACS sequences that binds to origin-recognition complex (ORC) denoted as ORC-ACS and non-replicating ACS sequences (nrACS), that are not bound by ORC. In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS motifs in the non-coding segments points to the locations of ORC-ACS which are found far away from the adjacent gene start position compared to nrACS thereby enabling an accessible environment for ORC-proteins. Our attempt is novel in considering the contextual view of ACS and its flanking region along with nucleosome positioning in the S. cerevisiae genome and may be useful for any computational prediction scheme. PMID:27508123

  12. Gene ontology-based protein function prediction by using sequence composition information.

    Science.gov (United States)

    Dong, Qiwen; Zhou, Shuigeng; Deng, Lei; Guan, Jihong

    2010-06-01

    The prediction of protein function is a difficult and important problem in computational biology. In this study, an efficient method is presented to predict protein function with sequence composition information. Four kinds of basic building blocks of protein sequences are investigated, including N-grams, binary profiles, PFAM domains and InterPro domains. The protein sequences are mapped into high-dimensional vectors by using the occurrence frequencies of each kind of building blocks. The resulting vectors are then taken as input to support vector machine to predict their function based on gene ontology. Experiments are conducted over the subset of GOA database. The experimental results show that the protein function can be predicted from primary sequence information. The method based on InterPro domains outperforms the other building blocks, and gets an overall accuracy of 0.87 and ROC score is 0.93. We also demonstrate that the use of feature extraction algorithms such as latent semantic analysis and nonnegative matrix factorization, can efficiently remove noise and improve the prediction efficiency without significantly degrading the performance. The results obtained here are helpful for the prediction of protein function by using only sequence information. PMID:19995340

  13. Molecular phylogeny of western Atlantic Farfantepenaeus and Litopenaeus shrimp based on mitochondrial 16S partial sequences.

    Science.gov (United States)

    Maggioni, R; Rogers, A D; Maclean, N; D'Incao, F

    2001-01-01

    Partial sequences for the 16S rRNA mitochondrial gene were obtained from 10 penaeid shrimp species: Farfantepenaeus paulensis, F. brasiliensis, F. subtilis, F. duorarum, F. aztecus, Litopenaeus schmitti, L. setiferus, and Xiphopenaeus kroyeri from the western Atlantic and L. vannamei and L. stylirostris from the eastern Pacific. Sequences were also obtained from an undescribed morphotype of pink shrimp (morphotype II) usually identified as F. subtilis. The phylogeny resulting from the 16S partial sequences showed that these species form two well-supported monophyletic clades consistent with the two genera proposed in a recent systematic review of the suborder Dendrobranchiata. This contrasted with conclusions drawn from recent molecular phylogenetic work on penaeid shrimps based on partial sequences of the mitochondrial COI region that failed to support recent revisions of the Dendrobranchiata based on morphological analysis. Consistent differences observed in the sequences for morphotype II, coupled with previous allozyme data, support the conclusion that this is a previously undescribed species of Farfantepenaeus. PMID:11161743

  14. DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment

    Directory of Open Access Journals (Sweden)

    Kaufmann Michael

    2005-03-01

    Full Text Available Abstract Background We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by these methods on data sets with global but weak similarity at the primary-sequence level. Results In the present paper, we discuss strengths and weaknesses of DIALIGN in view of the underlying objective function. Based on these results, we propose several heuristics to improve the segment-based alignment approach. For pairwise alignment, we implemented a fragment-chaining algorithm that favours chains of low-scoring local alignments over isolated high-scoring fragments. For multiple alignment, we use an improved greedy procedure that is less sensitive to spurious local sequence similarities. To evaluate our method on globally related protein families, we used the well-known database BAliBASE. For benchmarking tests on locally related sequences, we created a new reference database called IRMBASE which consists of simulated conserved motifs implanted into non-related random sequences. Conclusion On BAliBASE, our new program performs significantly better than the previous version of DIALIGN and is comparable to the standard global aligner CLUSTAL W, though it is outperformed by some newly developed programs that focus on global alignment. On the locally related test sets in IRMBASE, our method outperforms all other programs that we evaluated.

  15. Reproducible analysis of sequencing-based RNA structure probing data with user-friendly tools

    DEFF Research Database (Denmark)

    Kielpinski, Lukasz Jan; Sidiropoulos, Nikos; Vinther, Jeppe

    2015-01-01

    time also made analysis of the data challenging for scientists without formal training in computational biology. Here, we discuss different strategies for data analysis of massive parallel sequencing-based structure-probing data. To facilitate reproducible and standardized analysis of this type of data...

  16. Teaching Research Methodology Using a Project-Based Three Course Sequence Critical Reflections on Practice

    Science.gov (United States)

    Braguglia, Kay H.; Jackson, Kanata A.

    2012-01-01

    This article presents a reflective analysis of teaching research methodology through a three course sequence using a project-based approach. The authors reflect critically on their experiences in teaching research methods courses in an undergraduate business management program. The introduction of a range of specific techniques including student…

  17. Magnetism Teaching Sequences Based on an Inductive Approach for First-Year Thai University Science Students

    Science.gov (United States)

    Narjaikaew, Pattawan; Emarat, Narumon; Arayathanitkul, Kwan; Cowie, Bronwen

    2010-01-01

    The study investigated the impact on student motivation and understanding of magnetism of teaching sequences based on an inductive approach. The study was conducted in large lecture classes. A pre- and post-Conceptual Survey of Electricity and Magnetism was conducted with just fewer than 700 Thai undergraduate science students, before and after…

  18. Neural network predicts sequence of TP53 gene based on DNA chip

    DEFF Research Database (Denmark)

    Spicker, J.S.; Wikman, F.; Lu, M.L.;

    2002-01-01

    We have trained an artificial neural network to predict the sequence of the human TP53 tumor suppressor gene based on a p53 GeneChip. The trained neural network uses as input the fluorescence intensities of DNA hybridized to oligonucleotides on the surface of the chip and makes between zero and...

  19. The effect of task difficulty on eye movement sequences in multiple dimensions

    NARCIS (Netherlands)

    Dewhurst, Richard; Nyström, Marcus; Jarodzka, Halszka; Foulsham, Tom; Johansson, Roger; Holmqvist, Kenneth

    2012-01-01

    Dewhurst, R., Nyström, M., Jarodzka, H., Foulsham, T., Johansson, R., & Holmqvist, K. (2012, May). The effect of task difficulty on eye movement sequences in multiple dimensions. Presentation at the Scandinavian Workshop on Applied Eye Tracking, Stockholm, Sweden.

  20. CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L. methylation filtered genomic genespace sequences

    Directory of Open Access Journals (Sweden)

    Spraggins Thomas A

    2007-04-01

    Full Text Available Abstract Background Cowpea [Vigna unguiculata (L. Walp.] is one of the most important food and forage legumes in the semi-arid tropics because of its ability to tolerate drought and grow on poor soils. It is cultivated mostly by poor farmers in developing countries, with 80% of production taking place in the dry savannah of tropical West and Central Africa. Cowpea is largely an underexploited crop with relatively little genomic information available for use in applied plant breeding. The goal of the Cowpea Genomics Initiative (CGI, funded by the Kirkhouse Trust, a UK-based charitable organization, is to leverage modern molecular genetic tools for gene discovery and cowpea improvement. One aspect of the initiative is the sequencing of the gene-rich region of the cowpea genome (termed the genespace recovered using methylation filtration technology and providing annotation and analysis of the sequence data. Description CGKB, Cowpea Genespace/Genomics Knowledge Base, is an annotation knowledge base developed under the CGI. The database is based on information derived from 298,848 cowpea genespace sequences (GSS isolated by methylation filtering of genomic DNA. The CGKB consists of three knowledge bases: GSS annotation and comparative genomics knowledge base, GSS enzyme and metabolic pathway knowledge base, and GSS simple sequence repeats (SSRs knowledge base for molecular marker discovery. A homology-based approach was applied for annotations of the GSS, mainly using BLASTX against four public FASTA formatted protein databases (NCBI GenBank Proteins, UniProtKB-Swiss-Prot, UniprotKB-PIR (Protein Information Resource, and UniProtKB-TrEMBL. Comparative genome analysis was done by BLASTX searches of the cowpea GSS against four plant proteomes from Arabidopsis thaliana, Oryza sativa, Medicago truncatula, and Populus trichocarpa. The possible exons and introns on each cowpea GSS were predicted using the HMM-based Genscan gene predication program and the

  1. Effect of nitrification on phosphorus dissolving in a piggery effluent treated by a sequencing batch reactor

    OpenAIRE

    Daumer, M.L.; Béline, F.; Guiziou, F.; Spérandio, M

    2007-01-01

    The effect of the nitrification on dissolved phosphorus during the treatment of piggery wastewater by a modified sequencing batch reactor has been observed in a previous study. The high solid mineral phosphorus content in the piggery wastewater and the chemical mechanism induced by the fall in pH during the nitrification were proposed to explain this effect. In this work, trials using modified sequencing batch reactors were performed to study the influence of the amount of nitrified nitrogen ...

  2. Sequence effects in service bundles: Implications for service design and scheduling

    OpenAIRE

    Dixon, Michael J.; Verma, Rohit

    2013-01-01

    The article of record as published may be located at http://dx.doi.org/10.1016/j.jom.2012.12.002 Researchers in several academic disciplines have investigated the effect of the sequence of pleasure and pain on the customer in service, experience, or healthcare-related interactions. Specifically, past research from psychology, behavioral economics, and other related fields suggests that the sequence effect can significantly impact a customer’s overall impression of a service intera...

  3. Evolution of EF-hand calcium-modulated proteins. III. Exon sequences confirm most dendrograms based on protein sequences: calmodulin dendrograms show significant lack of parallelism

    Science.gov (United States)

    Nakayama, S.; Kretsinger, R. H.

    1993-01-01

    In the first report in this series we presented dendrograms based on 152 individual proteins of the EF-hand family. In the second we used sequences from 228 proteins, containing 835 domains, and showed that eight of the 29 subfamilies are congruent and that the EF-hand domains of the remaining 21 subfamilies have diverse evolutionary histories. In this study we have computed dendrograms within and among the EF-hand subfamilies using the encoding DNA sequences. In most instances the dendrograms based on protein and on DNA sequences are very similar. Significant differences between protein and DNA trees for calmodulin remain unexplained. In our fourth report we evaluate the sequences and the distribution of introns within the EF-hand family and conclude that exon shuffling did not play a significant role in its evolution.

  4. Use of polyphase continuous excitation based on the Frank sequence in EPR.

    Science.gov (United States)

    Tseitlin, Mark; Quine, Richard W; Eaton, Sandra S; Eaton, Gareth R

    2011-08-01

    Polyphase continuous excitation based on the Frank sequence is suggested as an alternative to single pulse excitation in EPR. The method allows reduction of the source power, while preserving the excitation bandwidth of a single pulse. For practical EPR implementation the use of a cross-loop resonator is essential to provide isolation between the spin system and the resonator responses to the excitation. Provided that a line broadening of about 5% is acceptable, the cumulative turning angle of the magnetization vector generated by the excitation sequence can be quite large and can produce signal amplitudes that are comparable to that achieved with a higher power 90° pulse. PMID:21737326

  5. A new RF tagging pulse based on the Frank poly-phase perfect sequence

    DEFF Research Database (Denmark)

    Laustsen, Christoffer; Greferath, Marcus; Ringgaard, Steffen;

    2014-01-01

    Radio frequency (RF) spectrally selective multiband pulses or tagging pulses, are applicable in a broad range of magnetic resonance methods. We demonstrate through simulations and experiments a new phase-modulation-only RF pulse for RF tagging based on the Frank poly-phase perfect sequence. In...... addition, we introduce an extended version with a WURST modulation (Frank-WURST). The new pulses exhibit interesting and flexible spin tagging properties and are easily implemented in existing MR sequences, where they can substitute slice-selective pulses with no additional alterations....

  6. Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes

    OpenAIRE

    Ruppitsch, Werner; Pietzka, Ariane; Prior, Karola; Bletz, Stefan; Fernandez, Haizpea Lasa; Allerberger, Franz; Harmsen, Dag; Mellmann, Alexander

    2015-01-01

    Whole-genome sequencing (WGS) has emerged today as an ultimate typing tool to characterize Listeria monocytogenes outbreaks. However, data analysis and interlaboratory comparability of WGS data are still challenging for most public health laboratories. Therefore, we have developed and evaluated a new L. monocytogenes typing scheme based on genome-wide gene-by-gene comparisons (core genome multilocus the sequence typing [cgMLST]) to allow for a unique typing nomenclature. Initially, we determi...

  7. DNAskew: Statistical Analysis of Base Compositional Asymmetry and Prediction of Replication Boundaries in the Genome Sequences

    Institute of Scientific and Technical Information of China (English)

    Xiang-RuMA; Shao-BoXIAO; Ai-ZhenGUO; Jian-QiangLUE; Huan-ChunCHEN

    2004-01-01

    Sueoka and Lobry declared respectively that, in the absence of bias between the two DNA strands for mutation and selection, the base composition within each strand should be A=T and C=G (this state is called Parity Rule type 2, PR2). However, the genome sequences of many bacteria, vertebrates and viruses showed asymmetries in base composition and gene direction. To determine the relationship of base composition skews with replication orientation, gene function, codon usage biases and phylogenetic evolution,in this paper a program called DNAskew was developed for the statistical analysis of strand asymmetry and codon composition bias in the DNA sequence. In addition, the program can also be used to predict the replication boundaries of genome sequences. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. DNAskew was written in Perl script language and implemented on the LINUX operating system. It works quickly with annotated or unannotated sequences in GBFF (GenBank flatfile) or fasta format. The source code is freely available for academic use at http://www.epizooty.com/pub/stat/DNAskew.

  8. Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis

    Science.gov (United States)

    Tinker, Nicholas A.; Bekele, Wubishet A.; Hattori, Jiro

    2016-01-01

    Genotyping-by-sequencing (GBS), and related methods, are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of single nucleotide polymorphisms (SNPs) within sequence tags. This provides a powerful and economical approach to whole-genome genotyping, facilitating applications in genomics, diversity analysis, and molecular breeding. However, due to the complexity of analyzing large data sets, applications of GBS may require substantial time, expertise, and computational resources. Haplotag, the novel GBS software described here, is freely available, and operates with minimal user-investment on widely available computer platforms. Haplotag is unique in fulfilling the following set of criteria: (1) operates without a reference genome; (2) can be used in a polyploid species; (3) provides a discovery mode, and a production mode; (4) discovers polymorphisms based on a model of tag-level haplotypes within sequenced tags; (5) reports SNPs as well as haplotype-based genotypes; and (6) provides an intuitive visual “passport” for each inferred locus. Haplotag is optimized for use in a self-pollinating plant species. PMID:26818073

  9. A pedigree-based study of mitochondrial D-loop DNA sequence variation among Arabian horses.

    Science.gov (United States)

    Bowling, A T; Del Valle, A; Bowling, M

    2000-02-01

    Through DNA sequence comparisons of a mitochondrial D-loop hypervariable region, we investigated matrilineal diversity for Arabian horses in the United States. Sixty-two horses were tested. From published pedigrees they traced in the maternal line to 34 mares acquired primarily in the mid to late 19th century from nomadic Bedouin tribes. Compared with the reference sequence (GenBank X79547), these samples showed 27 haplotypes with altogether 31 base substitution sites within 397 bp of sequence. Based on examination of pedigrees from a random sampling of 200 horses in current studbooks of the Arabian Horse Registry of America, we estimated that this study defined the expected mtDNA haplotypes for at least 89% of Arabian horses registered in the US. The reliability of the studbook recorded maternal lineages of Arabian pedigrees was demonstrated by haplotype concordance among multiple samplings in 14 lines. Single base differences observed within two maternal lines were interpreted as representing alternative fixations of past heteroplasmy. The study also demonstrated the utility of mtDNA sequence studies to resolve historical maternity questions without access to biological material from the horses whose relationship was in question, provided that representatives of the relevant female lines were available for comparison. The data call into question the traditional assumption that Arabian horses of the same strain necessarily share a common maternal ancestry. PMID:10690354

  10. Identification of Chlorophyceae based on 18S rDNA sequences from Persian Gulf.

    Directory of Open Access Journals (Sweden)

    Raheem Haddad

    2014-12-01

    Full Text Available Chlorophyceae are important constituents of marine phytoplankton. The taxonomy of Chlorophyceae was traditionally based solely on morphological characteristics. In the present research project, genetic diversity was investigated to analyze five species of Chlorophyceae from waters of the Persian Gulf.A clone library of the ribosomal small subunit RNA gene (18S rDNA in the nuclear genome was constructed by PCR, and then, after examining the clones, selected clones were sequenced. The determined clone sequences were analyzed by a similarity search of the NCBI GenBank database using BLAST.Eleven sequences were identified correctly and used for phylogenetic analysis. We identified species of Chlorophyta (Chlorella sorokiniana, Chlamydomonas sp., Neochloris aquatic, Picochlorum sp. and Nannochloris atomus without the need to conduct extensive colony isolation techniques. Therefore, this improved molecular method can be used to generate a robust database describing the species diversity of environmental samples.

  11. Tracing the Spread of Clostridium difficile Ribotype 027 in Germany Based on Bacterial Genome Sequences.

    Directory of Open Access Journals (Sweden)

    Matthias Steglich

    Full Text Available We applied whole-genome sequencing to reconstruct the spatial and temporal dynamics underpinning the expansion of Clostridium difficile ribotype 027 in Germany. Based on re-sequencing of genomes from 57 clinical C. difficile isolates, which had been collected from hospitalized patients at 36 locations throughout Germany between 1990 and 2012, we demonstrate that C. difficile genomes have accumulated sequence variation sufficiently fast to document the pathogen's spread at a regional scale. We detected both previously described lineages of fluoroquinolone-resistant C. difficile ribotype 027, FQR1 and FQR2. Using Bayesian phylogeographic analyses, we show that fluoroquinolone-resistant C. difficile 027 was imported into Germany at least four times, that it had been widely disseminated across multiple federal states even before the first outbreak was noted in 2007, and that it has continued to spread since.

  12. The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects.

    Science.gov (United States)

    Kamola, Piotr J; Nakano, Yuko; Takahashi, Tomoko; Wilson, Paul A; Ui-Tei, Kumiko

    2015-12-01

    RNA interference (RNAi) is a powerful tool for post-transcriptional gene silencing. However, the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA (miRNA) silencing. To better understand these off-target effects, we investigated the correlation between sequence features within various subsections of siRNA guide strands, and its corresponding target sequences, with off-target activities. Our results confirm previous reports that strength of base-pairing in the siRNA seed region is the primary factor determining the efficiency of off-target silencing. However, the degree of downregulation of off-target transcripts with shared seed sequence is not necessarily similar, suggesting that there are additional auxiliary factors that influence the silencing potential. Here, we demonstrate that both the melting temperature (Tm) in a subsection of siRNA non-seed region, and the GC contents of its corresponding target sequences, are negatively correlated with the efficiency of off-target effect. Analysis of experimentally validated miRNA targets demonstrated a similar trend, indicating a putative conserved mechanistic feature of seed region-dependent targeting mechanism. These observations may prove useful as parameters for off-target prediction algorithms and improve siRNA 'specificity' design rules. PMID:26657993

  13. Accounting for outliers and calendar effects in surrogate simulations of stock return sequences

    CERN Document Server

    Leontitsis, A; Leontitsis, Alexandros; Vorlow, Constantinos E.

    2005-01-01

    Surrogate Data Analysis (SDA) is a statistical hypothesis testing framework for the determination of weak chaos in time series dynamics. Existing SDA procedures do not account properly for the rich structures observed in stock return sequences, attributed to the presence of heteroscedasticity, seasonal effects and outliers. In this paper we suggest a modification of the SDA framework, based on the robust estimation of location and scale parameters of mean-stationary time series and a probabilistic framework which deals with outliers. A demonstration on the NASDAQ Composite index daily returns shows that the proposed approach produces surrogates that faithfully reproduce the structure of the original series while being manifestations of linear-random dynamics.

  14. Effects of Aftershock Declustering in Risk Modeling: Case Study of a Subduction Sequence in Mexico

    Science.gov (United States)

    Kane, D. L.; Nyst, M.

    2014-12-01

    Earthquake hazard and risk models often assume that earthquake rates can be represented by a stationary Poisson process, and that aftershocks observed in historical seismicity catalogs represent a deviation from stationarity that must be corrected before earthquake rates are estimated. Algorithms for classifying individual earthquakes as independent mainshocks or as aftershocks vary widely, and analysis of a single catalog can produce considerably different earthquake rates depending on the declustering method implemented. As these rates are propagated through hazard and risk models, the modeled results will vary due to the assumptions implied by these choices. In particular, the removal of large aftershocks following a mainshock may lead to an underestimation of the rate of damaging earthquakes and potential damage due to a large aftershock may be excluded from the model. We present a case study based on the 1907 - 1911 sequence of nine 6.9 Mexico in order to illustrate the variability in risk under various declustering approaches. Previous studies have suggested that subduction zone earthquakes in Mexico tend to occur in clusters, and this particular sequence includes events that would be labeled as aftershocks in some declustering approaches yet are large enough to produce significant damage. We model the ground motion for each event, determine damage ratios using modern exposure data, and then compare the variability in the modeled damage from using the full catalog or one of several declustered catalogs containing only "independent" events. We also consider the effects of progressive damage caused by each subsequent event and how this might increase or decrease the total losses expected from this sequence.

  15. Quantitative sequence-function relationships in proteins based on gene ontology

    Directory of Open Access Journals (Sweden)

    Lesk Arthur M

    2007-08-01

    Full Text Available Abstract Background The relationship between divergence of amino-acid sequence and divergence of function among homologous proteins is complex. The assumption that homologs share function – the basis of transfer of annotations in databases – must therefore be regarded with caution. Here, we present a quantitative study of sequence and function divergence, based on the Gene Ontology classification of function. We determined the relationship between sequence divergence and function divergence in 6828 protein families from the PFAM database. Within families there is a broad range of sequence similarity from very closely related proteins – for instance, orthologs in different mammals – to very distantly-related proteins at the limit of reliable recognition of homology. Results We correlated the divergence in sequences determined from pairwise alignments, and the divergence in function determined by path lengths in the Gene Ontology graph, taking into account the fact that many proteins have multiple functions. Our results show that, among homologous proteins, the proportion of divergent functions decreases dramatically above a threshold of sequence similarity at about 50% residue identity. For proteins with more than 50% residue identity, transfer of annotation between homologs will lead to an erroneous attribution with a totally dissimilar function in fewer than 6% of cases. This means that for very similar proteins (about 50 % identical residues the chance of completely incorrect annotation is low; however, because of the phenomenon of recruitment, it is still non-zero. Conclusion Our results describe general features of the evolution of protein function, and serve as a guide to the reliability of annotation transfer, based on the closeness of the relationship between a new protein and its nearest annotated relative.

  16. [Characterization of Black and Dichothrix Cyanobacteria Based on the 16S Ribosomal RNA Gene Sequence

    Science.gov (United States)

    Ortega, Maya

    2010-01-01

    My project focuses on characterizing different cyanobacteria in thrombolitic mats found on the island of Highborn Cay, Bahamas. Thrombolites are interesting ecosystems because of the ability of bacteria in these mats to remove carbon dioxide from the atmosphere and mineralize it as calcium carbonate. In the future they may be used as models to develop carbon sequestration technologies, which could be used as part of regenerative life systems in space. These thrombolitic communities are also significant because of their similarities to early communities of life on Earth. I targeted two cyanobacteria in my research, Dichothrix spp. and whatever black is, since they are believed to be important to carbon sequestration in these thrombolitic mats. The goal of my summer research project was to molecularly identify these two cyanobacteria. DNA was isolated from each organism through mat dissections and DNA extractions. I ran Polymerase Chain Reactions (PCR) to amplify the 16S ribosomal RNA (rRNA) gene in each cyanobacteria. This specific gene is found in almost all bacteria and is highly conserved, meaning any changes in the sequence are most likely due to evolution. As a result, the 16S rRNA gene can be used for bacterial identification of different species based on the sequence of their 16S rRNA gene. Since the exact sequence of the Dichothrix gene was unknown, I designed different primers that flanked the gene based on the known sequences from other taxonomically similar cyanobacteria. Once the 16S rRNA gene was amplified, I cloned the gene into specialized Escherichia coli cells and sent the gene products for sequencing. Once the sequence is obtained, it will be added to a genetic database for future reference to and classification of other Dichothrix sp.

  17. Comparison of pulse sequences for R1-based electron paramagnetic resonance oxygen imaging

    Science.gov (United States)

    Epel, Boris; Halpern, Howard J.

    2015-05-01

    Electron paramagnetic resonance (EPR) spin-lattice relaxation (SLR) oxygen imaging has proven to be an indispensable tool for assessing oxygen partial pressure in live animals. EPR oxygen images show remarkable oxygen accuracy when combined with high precision and spatial resolution. Developing more effective means for obtaining SLR rates is of great practical, biological and medical importance. In this work we compared different pulse EPR imaging protocols and pulse sequences to establish advantages and areas of applicability for each method. Tests were performed using phantoms containing spin probes with oxygen concentrations relevant to in vivo oxymetry. We have found that for small animal size objects the inversion recovery sequence combined with the filtered backprojection reconstruction method delivers the best accuracy and precision. For large animals, in which large radio frequency energy deposition might be critical, free induction decay and three pulse stimulated echo sequences might find better practical usage.

  18. A Real-Time de novo DNA Sequencing Assembly Platform Based on an FPGA Implementation.

    Science.gov (United States)

    Hu, Yuanqi; Georgiou, Pantelis

    2016-01-01

    This paper presents an FPGA based DNA comparison platform which can be run concurrently with the sensing phase of DNA sequencing and shortens the overall time needed for de novo DNA assembly. A hybrid overlap searching algorithm is applied which is scalable and can deal with incremental detection of new bases. To handle the incomplete data set which gradually increases during sequencing time, all-against-all comparisons are broken down into successive window-against-window comparison phases and executed using a novel dynamic suffix comparison algorithm combined with a partitioned dynamic programming method. The complete system has been designed to facilitate parallel processing in hardware, which allows real-time comparison and full scalability as well as a decrease in the number of computations required. A base pair comparison rate of 51.2 G/s is achieved when implemented on an FPGA with successful DNA comparison when using data sets from real genomes. PMID:27045828

  19. A Novel Method of Predicting Protein Disordered Regions Based on Sequence Features

    Directory of Open Access Journals (Sweden)

    Tong-Hui Zhao

    2013-01-01

    Full Text Available With a large number of disordered proteins and their important functions discovered, it is highly desired to develop effective methods to computationally predict protein disordered regions. In this study, based on Random Forest (RF, Maximum Relevancy Minimum Redundancy (mRMR, and Incremental Feature Selection (IFS, we developed a new method to predict disordered regions in proteins. The mRMR criterion was used to rank the importance of all candidate features. Finally, top 128 features were selected from the ranked feature list to build the optimal model, including 92 Position Specific Scoring Matrix (PSSM conservation score features and 36 secondary structure features. As a result, Matthews correlation coefficient (MCC of 0.3895 was achieved on the training set by 10-fold cross-validation. On the basis of predicting results for each query sequence by using the method, we used the scanning and modification strategy to improve the performance. The accuracy (ACC and MCC were increased by 4% and almost 0.2%, respectively, compared with other three popular predictors: DISOPRED, DISOclust, and OnD-CRF. The selected features may shed some light on the understanding of the formation mechanism of disordered structures, providing guidelines for experimental validation.

  20. Aquifer Vulnerability Assessment Based on Sequence Stratigraphic and (39) Ar Transport Modeling.

    Science.gov (United States)

    Sonnenborg, Torben O; Scharling, Peter B; Hinsby, Klaus; Rasmussen, Erik S; Engesgaard, Peter

    2016-03-01

    A large-scale groundwater flow and transport model is developed for a deep-seated (100 to 300 m below ground surface) sedimentary aquifer system. The model is based on a three-dimensional (3D) hydrostratigraphic model, building on a sequence stratigraphic approach. The flow model is calibrated against observations of hydraulic head and stream discharge while the credibility of the transport model is evaluated against measurements of (39) Ar from deep wells using alternative parameterizations of dispersivity and effective porosity. The directly simulated 3D mean age distributions and vertical fluxes are used to visualize the two-dimensional (2D)/3D age and flux distribution along transects and at the top plane of individual aquifers. The simulation results are used to assess the vulnerability of the aquifer system that generally has been assumed to be protected by thick overlaying clayey units and therefore proposed as future reservoirs for drinking water supply. The results indicate that on a regional scale these deep-seated aquifers are not as protected from modern surface water contamination as expected because significant leakage to the deeper aquifers occurs. The complex distribution of local and intermediate groundwater flow systems controlled by the distribution of the river network as well as the topographical variation (Tóth 1963) provides the possibility for modern water to be found in even the deepest aquifers. PMID:26018029

  1. Exome sequencing and array-based comparative genomic hybridisation analysis of preferential 6-methylmercaptopurine producers.

    Science.gov (United States)

    Chua, E W; Cree, S; Barclay, M L; Doudney, K; Lehnert, K; Aitchison, A; Kennedy, M A

    2015-10-01

    Preferential conversion of azathioprine or 6-mercaptopurine into methylated metabolites is a major cause of thiopurine resistance. To seek potentially Mendelian causes of thiopurine hypermethylation, we recruited 12 individuals who exhibited extreme therapeutic resistance while taking azathioprine or 6-mercaptopurine and performed whole-exome sequencing (WES) and copy-number variant analysis by array-based comparative genomic hybridisation (aCGH). Exome-wide variant filtering highlighted four genes potentially associated with thiopurine metabolism (ENOSF1 and NFS1), transport (SLC17A4) or therapeutic action (RCC2). However, variants of each gene were found only in two or three patients, and it is unclear whether these genes could influence thiopurine hypermethylation. Analysis by aCGH did not identify any unusual or pathogenic copy-number variants. This suggests that if causative mutations for the hypermethylation phenotype exist they may be heterogeneous, occurring in several different genes, or they may lie within regulatory regions not captured by WES. Alternatively, hypermethylation may arise from the involvement of multiple genes with small effects. To test this hypothesis would require recruitment of large patient samples and application of genome-wide association studies. PMID:25752523

  2. Toner Savings Based on Quasi-Random Sequences and a Perceptual Study for Green Printing.

    Science.gov (United States)

    Montrucchio, Bartolomeo; Ferrero, Renato

    2016-05-01

    Toner savings in monochromatic printing are an important target for improving green computing performance and more specifically green printing. In order to extend the lifetime of the printer cartridge, some options are available for laser printers, usually reducing the number of dots with respect to the normal print quality. However available algorithms and patents do not provide a method for dynamically adapting the percentage of toner savings to the required printing quality. In this paper, we introduce a new quasi-random sequence-based algorithm for reducing the number of dots in the printing process, able to achieve optimal discrepancy and low computational complexity, for all print quality levels. In order to reduce patterns in the removed dots, blue noise dithering is applied when the desired percentage of toner savings is moderate. The proposed solution can be easily implemented in the printer firmware, given its low computational complexity. In order to verify the results from a perceptual point of view, an extended test with 135 volunteers and more than 5000 comparisons has been performed, besides checking that toner is effectively saved. Results show that the proposed approach can produce a reduction of the perceived quality almost directly proportional to the number of monochromatic dots skipped, with only a reduced influence from the font used. The perceptual results are better in the proposal than in the previous approaches. The proposed algorithm appears to be a promising technique for improving green printing in monochromatic laser printers without using custom fonts. PMID:27116672

  3. Sequence-based prediction of protein-protein interaction sites with L1-logreg classifier.

    Science.gov (United States)

    Dhole, Kaustubh; Singh, Gurdeep; Pai, Priyadarshini P; Mondal, Sukanta

    2014-05-01

    Protein-protein interactions are of central importance for virtually every process in a living cell. Information about the interaction sites in proteins improves our understanding of disease mechanisms and can provide the basis for new therapeutic approaches. Since a multitude of unique residue-residue contacts facilitate the interactions, protein-protein interaction sites prediction has become one of the most important and challenging problems of computational biology. Although much progress in this field has been reported, this problem is yet to be satisfactorily solved. Here, a novel method (LORIS: L1-regularized LOgistic Regression based protein-protein Interaction Sites predictor) is proposed, that identifies interaction residues, using sequence features and is implemented via the L1-logreg classifier. Results show that LORIS is not only quite effective, but also, performs better than existing state-of-the art methods. LORIS, available as standalone package, can be useful for facilitating drug-design and targeted mutation related studies, which require a deeper knowledge of protein interactions sites. PMID:24486250

  4. A Cost-Effective Approach to Sequence Hundreds of Complete Mitochondrial Genomes.

    Science.gov (United States)

    Nunez, Joaquin C B; Oleksiak, Marjorie F

    2016-01-01

    We present a cost-effective approach to sequence whole mitochondrial genomes for hundreds of individuals. Our approach uses small reaction volumes and unmodified (non-phosphorylated) barcoded adaptors to minimize reagent costs. We demonstrate our approach by sequencing 383 Fundulus sp. mitochondrial genomes (192 F. heteroclitus and 191 F. majalis). Prior to sequencing, we amplified the mitochondrial genomes using 4-5 custom-made, overlapping primer pairs, and sequencing was performed on an Illumina HiSeq 2500 platform. After removing low quality and short sequences, 2.9 million and 2.8 million reads were generated for F. heteroclitus and F. majalis respectively. Individual genomes were assembled for each species by mapping barcoded reads to a reference genome. For F. majalis, the reference genome was built de novo. On average, individual consensus sequences had high coverage: 61-fold for F. heteroclitus and 57-fold for F. majalis. The approach discussed in this paper is optimized for sequencing mitochondrial genomes on an Illumina platform. However, with the proper modifications, this approach could be easily applied to other small genomes and sequencing platforms. PMID:27505419

  5. A Cost-Effective Approach to Sequence Hundreds of Complete Mitochondrial Genomes

    Science.gov (United States)

    Oleksiak, Marjorie F.

    2016-01-01

    We present a cost-effective approach to sequence whole mitochondrial genomes for hundreds of individuals. Our approach uses small reaction volumes and unmodified (non-phosphorylated) barcoded adaptors to minimize reagent costs. We demonstrate our approach by sequencing 383 Fundulus sp. mitochondrial genomes (192 F. heteroclitus and 191 F. majalis). Prior to sequencing, we amplified the mitochondrial genomes using 4–5 custom-made, overlapping primer pairs, and sequencing was performed on an Illumina HiSeq 2500 platform. After removing low quality and short sequences, 2.9 million and 2.8 million reads were generated for F. heteroclitus and F. majalis respectively. Individual genomes were assembled for each species by mapping barcoded reads to a reference genome. For F. majalis, the reference genome was built de novo. On average, individual consensus sequences had high coverage: 61-fold for F. heteroclitus and 57-fold for F. majalis. The approach discussed in this paper is optimized for sequencing mitochondrial genomes on an Illumina platform. However, with the proper modifications, this approach could be easily applied to other small genomes and sequencing platforms. PMID:27505419

  6. Genomic clones of bovine parvovirus: Construction and effect of deletions and terminal sequence inversions on infectivity

    International Nuclear Information System (INIS)

    Genomic clones of the autonomous parvovirus bovine parvovirus (BPV) were constructed by blunt-end ligation of reannealed virion plus and minus DNA strands into the plasmid pUC8. These clones were stable during propagation in Escherichia coli JM107. All clones tested were found to be infectious by the criteria of plaque titer and progressive cytophathic effect after transfection into bovine fetal lung cells. Sequencing of the recombinant plasmids demonstrated that all of the BPV inserts had left-end (3')-terminal deletions of up to 34 bases. Defective genomes could also be detected in the progeny DNA even though the infection was initiated with homogeneous, cloned DNA. Full-length genomic clones with 3' flip and 3' flop conformations were constructed and were found to have equal infectivity. Expression of capsid proteins from tranfected genomes was demonstrated by hemagglutination, indirect immunofluorescence, and immunoprecipitation of [35S]methionine-labeled cell lysates. Use of appropriate antiserum for immunoprecipitation showed the synthesis of BPV capsid and noncapsid proteins after transfection. Independently, a series of genomic clones with increasingly larger 3'-terminal deletions was prepared from separately subcloned 3'-terminal fragments. Transfection of these clones into bovine fetal lung cells revealed that deletions of up to 34 bases at the 3' end lowered but did not abolish infectivity, while deletions of greater than 52 bases were lethal. End-label analysis showed that the 34-base deletion was repaired to wild-type length in the progeny virus

  7. Unusual conformational effect exerted by Z-DNA upon its neighboring sequences.

    OpenAIRE

    Kohwi-Shigematsu, T; Manes, T; Kohwi, Y

    1987-01-01

    Supercoiled plasmid DNA harboring an insert of (dG-dC)16, a sequence known to form Z-DNA upon negative supercoiling, was reacted with chloroacetaldehyde. Chloroacetaldehyde, like bromoacetaldehyde, was found to be a specific probe for detecting unpaired DNA bases in supercoiled plasmid DNA. Under torsional stress (at bacterial superhelical density), chloroacetaldehyde reacted at multiple discrete regions within the neighboring sequences of the (dG-dC)16 insert. When the plasmid population was...

  8. Readjoiner: a fast and memory efficient string graph-based sequence assembler

    Directory of Open Access Journals (Sweden)

    Gonnella Giorgio

    2012-05-01

    Full Text Available Abstract Background Ongoing improvements in throughput of the next-generation sequencing technologies challenge the current generation of de novo sequence assemblers. Most recent sequence assemblers are based on the construction of a de Bruijn graph. An alternative framework of growing interest is the assembly string graph, not necessitating a division of the reads into k-mers, but requiring fast algorithms for the computation of suffix-prefix matches among all pairs of reads. Results Here we present efficient methods for the construction of a string graph from a set of sequencing reads. Our approach employs suffix sorting and scanning methods to compute suffix-prefix matches. Transitive edges are recognized and eliminated early in the process and the graph is efficiently constructed including irreducible edges only. Conclusions Our suffix-prefix match determination and string graph construction algorithms have been implemented in the software package Readjoiner. Comparison with existing string graph-based assemblers shows that Readjoiner is faster and more space efficient. Readjoiner is available at http://www.zbh.uni-hamburg.de/readjoiner.

  9. Multiplex amplicon sequencing for microbe identification in community-based culture collections.

    Science.gov (United States)

    Armanhi, Jaderson Silveira Leite; de Souza, Rafael Soares Correa; de Araújo, Laura Migliorini; Okura, Vagner Katsumi; Mieczkowski, Piotr; Imperial, Juan; Arruda, Paulo

    2016-01-01

    Microbiome analysis using metagenomic sequencing has revealed a vast microbial diversity associated with plants. Identifying the molecular functions associated with microbiome-plant interaction is a significant challenge concerning the development of microbiome-derived technologies applied to agriculture. An alternative to accelerate the discovery of the microbiome benefits to plants is to construct microbial culture collections concomitant with accessing microbial community structure and abundance. However, traditional methods of isolation, cultivation, and identification of microbes are time-consuming and expensive. Here we describe a method for identification of microbes in culture collections constructed by picking colonies from primary platings that may contain single or multiple microorganisms, which we named community-based culture collections (CBC). A multiplexing 16S rRNA gene amplicon sequencing based on two-step PCR amplifications with tagged primers for plates, rows, and columns allowed the identification of the microbial composition regardless if the well contains single or multiple microorganisms. The multiplexing system enables pooling amplicons into a single tube. The sequencing performed on the PacBio platform led to recovery near-full-length 16S rRNA gene sequences allowing accurate identification of microorganism composition in each plate well. Cross-referencing with plant microbiome structure and abundance allowed the estimation of diversity and abundance representation of microorganism in the CBC. PMID:27404280

  10. PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

    Directory of Open Access Journals (Sweden)

    Francisco Alexandre P

    2012-05-01

    Full Text Available Abstract Background With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

  11. incaRNAfbinv: a web server for the fragment-based design of RNA sequences.

    Science.gov (United States)

    Drory Retwitzer, Matan; Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme; Barash, Danny

    2016-07-01

    In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu.ac.il/incaRNAfbinv. PMID:27185893

  12. Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations.

    Science.gov (United States)

    Truong, Hoa T; Ramos, A Marcos; Yalcin, Feyruz; de Ruiter, Marjo; van der Poel, Hein J A; Huvenaars, Koen H J; Hogers, René C J; van Enckevort, Leonora J G; Janssen, Antoine; van Orsouw, Nathalie J; van Eijk, Michiel J T

    2012-01-01

    Conventional marker-based genotyping platforms are widely available, but not without their limitations. In this context, we developed Sequence-Based Genotyping (SBG), a technology for simultaneous marker discovery and co-dominant scoring, using next-generation sequencing. SBG offers users several advantages including a generic sample preparation method, a highly robust genome complexity reduction strategy to facilitate de novo marker discovery across entire genomes, and a uniform bioinformatics workflow strategy to achieve genotyping goals tailored to individual species, regardless of the availability of a reference sequence. The most distinguishing features of this technology are the ability to genotype any population structure, regardless whether parental data is included, and the ability to co-dominantly score SNP markers segregating in populations. To demonstrate the capabilities of SBG, we performed marker discovery and genotyping in Arabidopsis thaliana and lettuce, two plant species of diverse genetic complexity and backgrounds. Initially we obtained 1,409 SNPs for arabidopsis, and 5,583 SNPs for lettuce. Further filtering of the SNP dataset produced over 1,000 high quality SNP markers for each species. We obtained a genotyping rate of 201.2 genotypes/SNP and 58.3 genotypes/SNP for arabidopsis (n = 222 samples) and lettuce (n = 87 samples), respectively. Linkage mapping using these SNPs resulted in stable map configurations. We have therefore shown that the SBG approach presented provides users with the utmost flexibility in garnering high quality markers that can be directly used for genotyping and downstream applications. Until advances and costs will allow for routine whole-genome sequencing of populations, we expect that sequence-based genotyping technologies such as SBG will be essential for genotyping of model and non-model genomes alike. PMID:22662172

  13. Detection of methylation in promoter sequences by melting curve analysis-based semiquantitative real time PCR

    Directory of Open Access Journals (Sweden)

    Lázcoz Paula

    2008-02-01

    Full Text Available Abstract Background We present two melting curve analysis (MCA-based semiquantitative real time PCR techniques to detect the promoter methylation status of genes. The first, MCA-MSP, follows the same principle as standard MSP but it is performed in a real time thermalcycler with results being visualized in a melting curve. The second, MCA-Meth, uses a single pair of primers designed with no CpGs in its sequence. These primers amplify both unmethylated and methylated sequences. In clinical applications the MSP technique has revolutionized methylation detection by simplifying the analysis to a PCR-based protocol. MCA-analysis based techniques may be able to further improve and simplify methylation analyses by reducing starting DNA amounts, by introducing an all-in-one tube reaction and by eliminating a final gel stage for visualization of the result. The current study aimed at investigating the feasibility of both MCA-MSP and MCA-Meth in the analysis of promoter methylation, and at defining potential advantages and shortcomings in comparison to currently implemented techniques, i.e. bisulfite sequencing and standard MSP. Methods The promoters of the RASSF1A (3p21.3, BLU (3p21.3 and MGMT (10q26 genes were analyzed by MCA-MSP and MCA-Meth in 13 astrocytoma samples, 6 high grade glioma cell lines and 4 neuroblastoma cell lines. The data were compared with standard MSP and validated by bisulfite sequencing. Results Both, MCA-MSP and MCA-Meth, successfully determined promoter methylation. MCA-MSP provided information similar to standard MSP analyses. However the analysis was possible in a single tube and avoided the gel stage. MCA-Meth proved to be useful in samples with intermediate methylation status, reflected by a melting curve position shift in dependence on methylation extent. Conclusion We propose MCA-MSP and MCA-Meth as alternative or supplementary techniques to MSP or bisulfite sequencing.

  14. (14)N overtone NMR under MAS: signal enhancement using symmetry-based sequences and novel simulation strategies.

    Science.gov (United States)

    Haies, Ibraheem M; Jarvis, James A; Bentley, Harry; Heinmaa, Ivo; Kuprov, Ilya; Williamson, Philip T F; Carravetta, Marina

    2015-03-01

    Overtone (14)N NMR spectroscopy is a promising route for the direct detection of (14)N signals with good spectral resolution. Its application is currently limited, however, by the absence of efficient polarization techniques for overtone signal enhancement and the lack of efficient numerical simulation techniques to aid in both the development of new methods and the analysis and interpretation of experimental data. In this paper we report a novel method for the transfer of polarization from (1)H to the (14)N overtone using symmetry-based R-sequences that overcome many of the limitations of adiabatic approaches that have worked successfully on static samples. Refinement of these sequences and the analysis of the resulting spectra have been facilitated through the development of an efficient simulation strategy for (14)N overtone NMR spectroscopy of spinning samples, using effective Hamiltonians on top of Floquet and Fokker-Planck equations. PMID:25662410

  15. Individual SWCNT based ionic field effect transistor

    Science.gov (United States)

    Pang, Pei; He, Jin; Park, Jae Hyun; Krstic, Predrag; Lindsay, Stuart

    2011-03-01

    Here we report that the ionic current through a single-walled carbon nanotube (SWCNT) can be effectively gated by a perpendicular electrical field from a top gate electrode, working as ionic field effect transistor. Both our experiment and simulation confirms that the electroosmotic current (EOF) is the main component in the ionic current through the SWCNT and is responsible for the gating effect. We also studied the gating efficiency as a function of solution concentration and pH and demonstrated that the device can work effectively in the physiological relevant condition. This work opens the door to use CNT based nanofluidics for ion and molecule manipulation. This work was supported by the DNA Sequencing Technology Program of the National Human Genome Research Institute (1RC2HG005625-01, 1R21HG004770-01), Arizona Technology Enterprises and the Biodesign Institute.

  16. Two valuation questions in one survey: Is it a recipe for sequencing and instrument context effects?

    Science.gov (United States)

    Giraud, K.L.; Loomis, J.B.; Johnson, R.L.

    1999-01-01

    Economic theory suggests that willingness to pay for two goods independently offered should remain unchanged when the survey instrument changes slightly. Four survey treatments consisting of comprehensive good and a subset of that good were used. The surveys alternated in the question ordering and in the embedded good which accompanied the comprehensive good. We tested for sequencing and instrument context effects using both a combined and split sample designs. In the combined sample case we found some evidence to sequencing effects in the data containing the first subset good. Likelihood ratio tests indicated that sequencing did not effect scale or location of parameters. In the test for instrument context effects, evidence was found indicating context does effect willingness to pay estimates.

  17. Prediction of influenza B vaccine effectiveness from sequence data.

    Science.gov (United States)

    Pan, Yidan; Deem, Michael W

    2016-08-31

    Influenza is a contagious respiratory illness that causes significant human morbidity and mortality, affecting 5-15% of the population in a typical epidemic season. Human influenza epidemics are caused by types A and B, with roughly 25% of human cases due to influenza B. Influenza B is a single-stranded RNA virus with a high mutation rate, and both prior immune history and vaccination put significant pressure on the virus to evolve. Due to the high rate of viral evolution, the influenza B vaccine component of the annual influenza vaccine is updated, roughly every other year in recent years. To predict when an update to the vaccine is needed, an estimate of expected vaccine effectiveness against a range of viral strains is required. We here introduce a method to measure antigenic distance between the influenza B vaccine and circulating viral strains. The measure correlates well with effectiveness of the influenza B component of the annual vaccine in humans between 1979 and 2014. We discuss how this measure of antigenic distance may be used in the context of annual influenza vaccine design and prediction of vaccine effectiveness. PMID:27473305

  18. SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data.

    Science.gov (United States)

    Steyaert, Sandra; Van Criekinge, Wim; De Paepe, Ayla; Denil, Simon; Mensaert, Klaas; Vandepitte, Katrien; Vanden Berghe, Wim; Trooskens, Geert; De Meyer, Tim

    2014-11-10

    Monoallelic gene expression is typically initiated early in the development of an organism. Dysregulation of monoallelic gene expression has already been linked to several non-Mendelian inherited genetic disorders. In humans, DNA-methylation is deemed to be an important regulator of monoallelic gene expression, but only few examples are known. One important reason is that current, cost-affordable truly genome-wide methods to assess DNA-methylation are based on sequencing post-enrichment. Here, we present a new methodology based on classical population genetic theory, i.e. the Hardy-Weinberg theorem, that combines methylomic data from MethylCap-seq with associated SNP profiles to identify monoallelically methylated loci. Applied on 334 MethylCap-seq samples of very diverse origin, this resulted in the identification of 80 genomic regions featured by monoallelic DNA-methylation. Of these 80 loci, 49 are located in genic regions of which 25 have already been linked to imprinting. Further analysis revealed statistically significant enrichment of these loci in promoter regions, further establishing the relevance and usefulness of the method. Additional validation was done using both 14 whole-genome bisulfite sequencing data sets and 16 mRNA-seq data sets. Importantly, the developed approach can be easily applied to other enrichment-based sequencing technologies, like the ChIP-seq-based identification of monoallelic histone modifications. PMID:25237057

  19. Base- level Chang and Sequence Stratigraphy of Lishu Fault Lacustrine Basin

    Institute of Scientific and Technical Information of China (English)

    Wang Simin; Liu Zhaojun; Liu Kui

    2000-01-01

    Base - level is a kind of surface which controls sedimentation and erosion. So, it can be concluded that it is baselevel change that controls the formation and internal structure of a sequence. A single cycle of base- level change can generate four sets of different stacking patterns. They are two sets of aggradation, one progradation and one retrogradation, which affects the features of the internal structure of a sequence. Lishu fault subsidence of Songliao basin is a typical half - graben lacustrine basin. Comprehensive base - level change analysis indicates that six base - level cycles and their related six sequences can be recognized between T4 and T5 seismic reflection surface. The contemporaneous fault is the main controlling factor of the fault lacustrine basin. There are obvious differences exist in the composition of sedimentary systems and all systems tracts between its steep slope (the side that basin control fault existed) and flat slope. Except highstand systems tract is composed of fan delta - lacustrine system, lowstand systems tract, transgressive systems tract and regressive systems tract are all made up of fan delta - underwater fan- lacustrine sedimentary systems in the side of steep slope.

  20. Dual mechanisms of DNA sequencing based on tunnelling between nitrogen-doped carbon nanotube electrodes

    Science.gov (United States)

    Kim, Han; Kim, Yong-Hoon

    2013-03-01

    The DNA sequencing approach based on the combination of nanopores and electron tunnelling has seen considerable advances in recent years, and particularly carbon nanomaterials have emerged as promising candidates to replace metal electrodes. Carrying out extensive first-principles calculations, we here show that two distinct DNA sequencing mechanisms can be achieved with different configurations of a single-type nitrogen-doped capped carbon nanotube (CNT) that has significantly enhanced transmission and chemical sensitivity over its pristine counterpart. With a small CNT-CNT gap size that induces face-on nucleobase configurations, we obtain a typical conductance ordering where the largest signal is induced from guanine due to its highest occupied molecular orbital energetic position higher than those of other bases. On the other hand, for a large CNT-CNT gap size that accommodates edge-on nucleobase configurations, we extract a completely different conductance ordering in which thymine results in the largest signal. We find that the latter novel nucleobase sensing mechanism originates from the nature of chemical connectivity between nitrogen-doped CNT caps and nucleobase functional groups that include the thymine methyl group. This work thus demonstrates the feasibility of a tunnelling-based dual-mode approach toward whole genome sequencing applications, detection of DNA base modifications, and single-molecule sensing in general.

  1. On-line integration of PCR and cycle sequencing in capillaries: from human genomic DNA directly to called bases

    OpenAIRE

    Hashimoto, Masahiko; He, Yan; Yeung, Edward S.

    2003-01-01

    A fully integrated system has been developed for genetic analysis based on direct sequencing of polymerase chain reaction (PCR) products. The instrument is based on a serially connected fused-silica capillary assembly. The technique involves the use of microreactors for small-volume PCR and for dye-terminator cycle-sequencing reaction, purification of the sequencing fragments, and separation of the purified DNA ladder. Four modifications to the normal PCR protocol allow the elimination of pos...

  2. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    OpenAIRE

    Lees Jonathan G; Janes Robert W

    2008-01-01

    Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction method...

  3. A unified mixed-effects model for rare-variant association in sequencing studies.

    Science.gov (United States)

    Sun, Jianping; Zheng, Yingye; Hsu, Li

    2013-05-01

    For rare-variant association analysis, due to extreme low frequencies of these variants, it is necessary to aggregate them by a prior set (e.g., genes and pathways) in order to achieve adequate power. In this paper, we consider hierarchical models to relate a set of rare variants to phenotype by modeling the effects of variants as a function of variant characteristics while allowing for variant-specific effect (heterogeneity). We derive a set of two score statistics, testing the group effect by variant characteristics and the heterogeneity effect. We make a novel modification to these score statistics so that they are independent under the null hypothesis and their asymptotic distributions can be derived. As a result, the computational burden is greatly reduced compared with permutation-based tests. Our approach provides a general testing framework for rare variants association, which includes many commonly used tests, such as the burden test [Li and Leal, 2008] and the sequence kernel association test [Wu et al., 2011], as special cases. Furthermore, in contrast to these tests, our proposed test has an added capacity to identify which components of variant characteristics and heterogeneity contribute to the association. Simulations under a wide range of scenarios show that the proposed test is valid, robust, and powerful. An application to the Dallas Heart Study illustrates that apart from identifying genes with significant associations, the new method also provides additional information regarding the source of the association. Such information may be useful for generating hypothesis in future studies. PMID:23483651

  4. Sequence effects in structures of the dinucleotides d-pApT and d-pTpA

    International Nuclear Information System (INIS)

    The H1', H2' and H2 regions of the 270-MHz PMR spectra of two deoxydinucleotides, d-pTpA an d-pApT, have been analyzed. The coupling constants in the sugar ring indicate that both A and T sugars have a tendency to acquire 2E conformations. There is also a marginal difference in the 2E populations of the T sugar in the two dinucleotides. The trends in the chemical shifts of base protons indicate different stacking of the bases in d-pApT and d-pTpA. The sequence effects on base stacking and pentose conformation are discussed. (orig.)

  5. Congruency sequence effect in cross-task context: evidence for dimension-specific modulation.

    Science.gov (United States)

    Lee, Jaeyong; Cho, Yang Seok

    2013-11-01

    The congruency sequence effect refers to a reduced congruency effect after incongruent trials relative to congruent trials. This modulation is thought to be, at least in part, due to the control mechanisms resolving conflict. The present study examined the nature of the control mechanisms by having participants perform two different tasks in an alternating way. When participants performed horizontal and vertical Simon tasks in Experiment 1A, and horizontal and vertical spatial Stroop task in Experiment 1B, no congruency sequence effect was obtained between the task congruencies. When the Simon task and spatial Stroop task were performed with different response sets in Experiment 2, no congruency sequence effect was obtained. However, in Experiment 3, in which the participants performed the horizontal Simon and spatial Stroop tasks with an identical response set, a significant congruency sequence effect was obtained between the task congruencies. In Experiment 4, no congruency sequence effect was obtained when participants performed two tasks having different task-irrelevant dimensions with the identical response set. The findings suggest inhibitory processing between the task-irrelevant dimension and response mode after conflict. PMID:24184348

  6. Heterogeneous Suppression of Sequential Effects in Random Sequence Generation, but Not in Operant Learning

    Science.gov (United States)

    Shteingart, Hanan; Loewenstein, Yonatan

    2016-01-01

    There is a long history of experiments in which participants are instructed to generate a long sequence of binary random numbers. The scope of this line of research has shifted over the years from identifying the basic psychological principles and/or the heuristics that lead to deviations from randomness, to one of predicting future choices. In this paper, we used generalized linear regression and the framework of Reinforcement Learning in order to address both points. In particular, we used logistic regression analysis in order to characterize the temporal sequence of participants’ choices. Surprisingly, a population analysis indicated that the contribution of the most recent trial has only a weak effect on behavior, compared to more preceding trials, a result that seems irreconcilable with standard sequential effects that decay monotonously with the delay. However, when considering each participant separately, we found that the magnitudes of the sequential effect are a monotonous decreasing function of the delay, yet these individual sequential effects are largely averaged out in a population analysis because of heterogeneity. The substantial behavioral heterogeneity in this task is further demonstrated quantitatively by considering the predictive power of the model. We show that a heterogeneous model of sequential dependencies captures the structure available in random sequence generation. Finally, we show that the results of the logistic regression analysis can be interpreted in the framework of reinforcement learning, allowing us to compare the sequential effects in the random sequence generation task to those in an operant learning task. We show that in contrast to the random sequence generation task, sequential effects in operant learning are far more homogenous across the population. These results suggest that in the random sequence generation task, different participants adopt different cognitive strategies to suppress sequential dependencies when

  7. Pigs in Sequence Space: A 0.66X Coverage Pig Genome Survey based on Shotgun Sequencing

    DEFF Research Database (Denmark)

    Wernersson, R; Schierup, Mikkel Heide; Jørgensen, Frank Grønlund;

    2005-01-01

    to the structure in human. Conclusion The addition of the pig to the set of species sequenced at low coverage adds to the understanding of selective pressures that have acted on the human genome by bisecting the evolutionary branch between human and mouse with the mouse branch being approximately 3 times as long...

  8. State of the art and challenges in sequence based T-cell epitope prediction

    DEFF Research Database (Denmark)

    Lundegaard, Claus; Hoof, Ilka; Lund, Ole;

    2010-01-01

    field has evolved significantly. Methods have now been developed that produce highly accurate binding predictions for many alleles and integrate both proteasomal cleavage and transport events. Moreover have so-called pan-specific methods been developed, which allow for prediction of peptide binding to......Sequence based T-cell epitope predictions have improved immensely in the last decade. From predictions of peptide binding to major histocompatibility complex molecules with moderate accuracy, limited allele coverage, and no good estimates of the other events in the antigen-processing pathway, the...... MHC alleles characterized by limited or no peptide binding data. Most of the developed methods are publicly available, and have proven to be very useful as a shortcut in epitope discovery. Here, we will go through some of the history of sequence-based predictions of helper as well as cytotoxic T cell...

  9. Detecting Protein-Protein Interactions with a Novel Matrix-Based Protein Sequence Representation and Support Vector Machines

    Directory of Open Access Journals (Sweden)

    Zhu-Hong You

    2015-01-01

    Full Text Available Proteins and their interactions lie at the heart of most underlying biological processes. Consequently, correct detection of protein-protein interactions (PPIs is of fundamental importance to understand the molecular mechanisms in biological systems. Although the convenience brought by high-throughput experiment in technological advances makes it possible to detect a large amount of PPIs, the data generated through these methods is unreliable and may not be completely inclusive of all possible PPIs. Targeting at this problem, this study develops a novel computational approach to effectively detect the protein interactions. This approach is proposed based on a novel matrix-based representation of protein sequence combined with the algorithm of support vector machine (SVM, which fully considers the sequence order and dipeptide information of the protein primary sequence. When performed on yeast PPIs datasets, the proposed method can reach 90.06% prediction accuracy with 94.37% specificity at the sensitivity of 85.74%, indicating that this predictor is a useful tool to predict PPIs. Achieved results also demonstrate that our approach can be a helpful supplement for the interactions that have been detected experimentally.

  10. Compensation of negative sequence stator flux of doubly-fed induction generator using polar voltage control-based direct torque control under unbalanced grid voltage condition

    Directory of Open Access Journals (Sweden)

    Badrinarayan Bansilal Pimple

    2015-02-01

    Full Text Available This study proposes a polar voltage control-based direct torque control method to reduce the effects of unbalanced grid voltage on doubly-fed induction generator (DFIG-based wind turbine system. Under unbalanced grid voltage, the stator flux has a negative sequence component which leads to second harmonic pulsation in torque, stator active power, stator reactive power, stator current and rotor current. In the control scheme, the negative sequence rotor voltage vector is controlled to compensate the negative sequence stator flux by negative sequence rotor flux. Simulation study is carried out on a 2 MW DFIG system using MATLAB/SIMULINK. Feasibility of the proposed control strategy is experimentally verified on a 1.5 kW DFIG system.

  11. RGB Color Model Based the Fire Detection Algorithm in Video Sequences on Wireless Sensor Network

    OpenAIRE

    Yoon-Ho Kim; Alla Kim; Hwa-Young Jeong

    2014-01-01

    Since the fire causes serious disasters, fire detection has been an important study to protect human life. Based on the deficiencies of existing fire detection on real-time and monitoring accuracy, the wireless sensor network technique for fire detection was introduced and needed. In this paper, we proposed the fire detection algorithm in video sequences on wireless sensor network. The proposed fire detection algorithm processes visual information acquired through static camera that lets us i...

  12. Rapid Detection and Identification of Infectious Pathogens Based on High-throughput Sequencing

    OpenAIRE

    Pei-Xiang Ni; Xin Ding; Yin-Xin Zhang; Xue Yao; Rui-Xue Sun; Peng Wang; Yan-Ping Gong; Jia-Li Zhou; Dong-Fang Li; Hong-Long Wu; Xin Yi; Ling Yang; Yun Long

    2015-01-01

    Background: The dilemma of pathogens identification in patients with unidentified clinical symptoms such as fever of unknown origin exists, which not only poses a challenge to both the diagnostic and therapeutic process by itself, but also to expert physicians. Methods: In this report, we have attempted to increase the awareness of unidentified pathogens by developing a method to investigate hitherto unidentified infectious pathogens based on unbiased high-throughput sequencing. Resul...

  13. Use of polyphase continuous excitation based on the Frank sequence in EPR.

    OpenAIRE

    Tseitlin, Mark; Quine, Richard W.; Eaton, Sandra S.; Eaton, Gareth R.

    2011-01-01

    Polyphase continuous excitation based on the Frank sequence is suggested as an alternative to single pulse excitation in EPR. The method allows reduction of the source power, while preserving the excitation bandwidth of a single pulse. For practical EPR implementation the use of a cross-loop resonator is essential to provide isolation between the spin system and the resonator responses to the excitation. Provided that a line broadening of about 5% is acceptable, the cumulative turning angle o...

  14. Diagnostic distinction between anencephaly and amnion rupture sequence based on skeletal analysis.

    OpenAIRE

    Keeling, J W; Kjaer, I

    1994-01-01

    The axial skeletal development of eight second trimester aborted fetuses, clinically diagnosed as amnion rupture sequence with cranial involvement, was examined radiographically and histologically. Three of the eight fetuses showed axial skeletal malformation in the spine and the craniofacial skeleton corresponding to the malformations seen in anencephaly. These are vertebral body malformations, consisting of double corpora and of osseous malformations in the components of the cranial base, t...

  15. Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences

    OpenAIRE

    Ogilvie, Lesley A.; Bowler, Lucas D.; Caplin, Jonathan; Dedi, Cinzia; Diston, David; Cheek, Elizabeth; Taylor, Huw; Ebdon, James E.; Jones, Brian V.

    2013-01-01

    Bacterial viruses (bacteriophages) have a key role in shaping the development and functional outputs of host microbiomes. Although metagenomic approaches have greatly expanded our understanding of the prokaryotic virosphere, additional tools are required for the phage-oriented dissection of metagenomic data sets, and host-range affiliation of recovered sequences. Here we demonstrate the application of a genome signature-based approach to interrogate conventional whole-community metagenomes an...

  16. Evaluation of Repetitive Element Sequence-Based PCR as a Molecular Typing Method for Clostridium difficile

    OpenAIRE

    Spigaglia, Patrizia; Mastrantonio, Paola

    2003-01-01

    Repetitive element sequence-based PCR (rep-PCR) is a typing method that enables the generation of DNA fingerprinting that discriminates bacterial strains. In this study, we evaluated the applicability of rep-PCR in typing Clostridium difficile clinical isolates. The results obtained by rep-PCR were compared with those obtained by pulsed-field gel electrophoresis (PFGE) and PCR ribotyping. A high correspondence between pattern differentiations produced by rep-PCR and PFGE was observed, whereas...

  17. SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data

    OpenAIRE

    Steyaert, Sandra; Van Criekinge, Wim; De Paepe, Ayla; Denil, Simon; Mensaert, Klaas; Vandepitte, Katrien; Vanden Berghe, Wim; Trooskens, Geert; de Meyer, Tim

    2014-01-01

    Monoallelic gene expression is typically initiated early in the development of an organism. Dysregulation of monoallelic gene expression has already been linked to several non-Mendelian inherited genetic disorders. In humans, DNA-methylation is deemed to be an important regulator of monoallelic gene expression, but only few examples are known. One important reason is that current, cost-affordable truly genome-wide methods to assess DNA-methylation are based on sequencing post-enrichment. Here...

  18. Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences

    OpenAIRE

    Michelle Klein Sercundes; Samantha Yuri Oshiro Branco Valadas; Lara Borges Keid; Tricia Maria Ferreira Souza Oliveira; Helena Lage Ferreira; Ricardo Wagner Almeida Vitor; Fábio Gregori; Rodrigo Martins Soares

    2016-01-01

    Abstract Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC) and beta subunit of RNA polymerase (rpoB), and mitochondrial gene coding for cytochrome B (cytB) were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula ...

  19. A reactive navigation method based on an incremental learning of tasks sequences

    OpenAIRE

    Davesne, Frédéric; Barret, Claude

    1999-01-01

    National audience Within the contest of learning sequences of basic tasks to build a complex behavior, a method is proposed to coordinate a hierarchical set of tasks. Each one possesses a set of sub-tasks lower in the hierarchy, which must be coordinated to respect a binary perceptive constraint. For each task, the coordination is achieved by a reinforcement learning inspired algorithm based on the heuristic which does not need internal parameters. A validation of the method is given, usin...

  20. Structural protein descriptors in 1-dimension and their sequence-based predictions.

    Science.gov (United States)

    Kurgan, Lukasz; Disfani, Fatemeh Miri

    2011-09-01

    The last few decades observed an increasing interest in development and application of 1-dimensional (1D) descriptors of protein structure. These descriptors project 3D structural features onto 1D strings of residue-wise structural assignments. They cover a wide-range of structural aspects including conformation of the backbone, burying depth/solvent exposure and flexibility of residues, and inter-chain residue-residue contacts. We perform first-of-its-kind comprehensive comparative review of the existing 1D structural descriptors. We define, review and categorize ten structural descriptors and we also describe, summarize and contrast over eighty computational models that are used to predict these descriptors from the protein sequences. We show that the majority of the recent sequence-based predictors utilize machine learning models, with the most popular being neural networks, support vector machines, hidden Markov models, and support vector and linear regressions. These methods provide high-throughput predictions and most of them are accessible to a non-expert user via web servers and/or stand-alone software packages. We empirically evaluate several recent sequence-based predictors of secondary structure, disorder, and solvent accessibility descriptors using a benchmark set based on CASP8 targets. Our analysis shows that the secondary structure can be predicted with over 80% accuracy and segment overlap (SOV), disorder with over 0.9 AUC, 0.6 Matthews Correlation Coefficient (MCC), and 75% SOV, and relative solvent accessibility with PCC of 0.7 and MCC of 0.6 (0.86 when homology is used). We demonstrate that the secondary structure predicted from sequence without the use of homology modeling is as good as the structure extracted from the 3D folds predicted by top-performing template-based methods. PMID:21787299

  1. Changes in DNA base sequence induced by targeted mutagenesis of lambda phage by ultraviolet light

    International Nuclear Information System (INIS)

    In targeted mutagenesis of lambda phage by ultraviolet light, the mutations are caused by radiation-induced lesions in the phage DNA. Of 62 mutations in the lambda cI gene that were sequenced, 41 of the targeted mutations were transitions, with similar numbers of C.G to T.A and T.A to C.G base changes. The remaining 21 mutations were about equally divided among eight transversions, seven frameshifts (5 additions and 2 deletions), and six double events with either two nearby base changes or a base change and a nearby frameshift. Of the 62 mutations, 60 could be associated with -Pyr-Pyr- sequences in the DNA, sites of likely photoproducts. For more information on this point, lambda phage were irradiated with 313 nm light in the presence of acetophenone for which the major photoproduct is reported to be the thymine-thymine cyclobutyl dimer, with no measurable Pyr(6-4)Pyo photoproducts. Of 22 mutations sequenced, 19 were transversions and only one was a transition, permitting the conclusion that thymine-thymine cyclobutyl dimers are not the primary cause of ultraviolet light-induced transitions. A consideration of all the data strongly suggests that Pyr(6-4)Pyo photoproducts are mutagenic lesions. (author)

  2. Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing

    Directory of Open Access Journals (Sweden)

    Baumbach Jan

    2007-10-01

    Full Text Available Abstract Background Detecting groups of functionally related proteins from their amino acid sequence alone has been a long-standing challenge in computational genome research. Several clustering approaches, following different strategies, have been published to attack this problem. Today, new sequencing technologies provide huge amounts of sequence data that has to be efficiently clustered with constant or increased accuracy, at increased speed. Results We advocate that the model of weighted cluster editing, also known as transitive graph projection is well-suited to protein clustering. We present the FORCE heuristic that is based on transitive graph projection and clusters arbitrary sets of objects, given pairwise similarity measures. In particular, we apply FORCE to the problem of protein clustering and show that it outperforms the most popular existing clustering tools (Spectral clustering, TribeMCL, GeneRAGE, Hierarchical clustering, and Affinity Propagation. Furthermore, we show that FORCE is able to handle huge datasets by calculating clusters for all 192 187 prokaryotic protein sequences (66 organisms obtained from the COG database. Finally, FORCE is integrated into the corynebacterial reference database CoryneRegNet. Conclusion FORCE is an applicable alternative to existing clustering algorithms. Its theoretical foundation, weighted cluster editing, can outperform other clustering paradigms on protein homology clustering. FORCE is open source and implemented in Java. The software, including the source code, the clustering results for COG and CoryneRegNet, and all evaluation datasets are available at http://gi.cebitec.uni-bielefeld.de/comet/force/.

  3. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

    Science.gov (United States)

    Lee, Wan-Ping; Stromberg, Michael P; Ward, Alistair; Stewart, Chip; Garrison, Erik P; Marth, Gabor T

    2014-01-01

    MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me). PMID:24599324

  4. Phylogenetic analyses of some genera in Oedipodidae (Orthoptera: Acridoidea) based on 16S mitochondrial partialgene sequences

    Institute of Scientific and Technical Information of China (English)

    Xiang-Chu Yin; Xin-Jiang Li; Wen-Qiang Wang; Hong Yin; Cheng-Quan Cao; Bao-Hua Ye; Zhan Yin

    2008-01-01

    Based on the 16S mitochondrial partial gene sequences of 29 genera, containing 26 from Oedipodidae and one each from Tanaoceridae, Pyrgomorphidae and Tetrigidae (as outgroups), the homologus sequences were compared and phylogenetic analyses were performed. A phylogenetic tree was inferred by neighbor-joining (N J). The results of sequences compared show that: (i) in a total of 574 bp of Oedipodidae, the number of substituted nucleotides was 265 bp and the average percentages ofT, C, A and G were 38.3%,11.4%, 31.8% and 18.5%, respectively, and the content of A+T (70.1%) was distinctly richer than that of C+G (29.9%); and (ii) the average nucleotide divergence of 16S rDNA sequences among genera of Oedipodidae were 9.0%, among families of Acridoidea were 17.0%, and between superfamilies (Tetrigoidea and Acridoidea) were 23.9%, respectively. The phylogenetic tree indicated: (i) the Oedipodidae was a monophyletic group, which suggested that the taxonomic status of this family was confLrrned; (ii) the genus Heteropternis separated from the other Oedipodids first and had another unique sound-producing structure in morphology, which is the type-genus of subfamily Heteropterninae; and (iii) the relative intergeneric relationship within the same continent was closer than that of different continents, and between the Eurasian genera and the African genera, was closer than that between Eurasians and Americans.

  5. A web-based search engine for triplex-forming oligonucleotide target sequences.

    Science.gov (United States)

    Gaddis, Sara S; Wu, Qi; Thames, Howard D; DiGiovanni, John; Walborg, Earl F; MacLeod, Michael C; Vasquez, Karen M

    2006-01-01

    Triplex technology offers a useful approach for site-specific modification of gene structure and function both in vitro and in vivo. Triplex-forming oligonucleotides (TFOs) bind to their target sites in duplex DNA, thereby forming triple-helical DNA structures via Hoogsteen hydrogen bonding. TFO binding has been demonstrated to site-specifically inhibit gene expression, enhance homologous recombination, induce mutation, inhibit protein binding, and direct DNA damage, thus providing a tool for gene-specific manipulation of DNA. We have developed a flexible web-based search engine to find and annotate TFO target sequences within the human and mouse genomes. Descriptive information about each site, including sequence context and gene region (intron, exon, or promoter), is provided. The engine assists the user in finding highly specific TFO target sequences by eliminating or flagging known repeat sequences and flagging overlapping genes. A convenient way to check for the uniqueness of a potential TFO binding site is provided via NCBI BLAST. The search engine may be accessed at spi.mdanderson.org/tfo. PMID:16764543

  6. GIPS: A Software Guide to Sequencing-Based Direct Gene Cloning in Forward Genetics Studies.

    Science.gov (United States)

    Hu, Han; Wang, Weitao; Zhu, Zhongxu; Zhu, Jianhua; Tan, Deyong; Zhou, Zhipeng; Mao, Chuanzao; Chen, Xin

    2016-04-01

    The Gene Identification via Phenotype Sequencing (GIPS) software considers a range of experimental and analysis choices in sequencing-based forward genetics studies within an integrated probabilistic framework, which enables direct gene cloning from the sequencing of several unrelated mutants of the same phenotype without the need to create segregation populations. GIPS estimates four measurements to help optimize an analysis procedure as follows: (1) the chance of reporting the true phenotype-associated gene; (2) the expected number of random genes that may be reported; (3) the significance of each candidate gene's association with the phenotype; and (4) the significance of violating the Mendelian assumption if no gene is reported or if all candidate genes have failed validation. The usage of GIPS is illustrated with the identification of a rice (Oryza sativa) gene that epistatically suppresses the phenotype of the phosphate2 mutant from sequencing three unrelated ethyl methanesulfonate mutants. GIPS is available at https://github.com/synergy-zju/gips/wiki with the user manual and an analysis example. PMID:26842621

  7. A STUDY ON SUBSTITUTION AND SEQUENCING EFFECTS USING CHECK-OFF MECHANISM

    OpenAIRE

    Rudra, Bidisha; Keeler, Andrew G.; McIntosh, Christopher S.

    1999-01-01

    Voluntary donations to non-game species protection through state income tax checkoffs are analyzed. An analogy between the contingent valuation method and check-off scheme is drawn by observing the existence of agenda effects in the latter. Results reveal that substitution and sequencing effects exist between species protection and other public goods.

  8. Comparison of Pulse Sequences for R1–based Electron Paramagnetic Resonance Oxygen Imaging

    OpenAIRE

    Epel, Boris; Halpern, Howard J.

    2015-01-01

    Electron paramagnetic resonance (EPR) spin-lattice relaxation (SLR) oxygen imaging has proven to be an indispensable tool for assessing oxygen partial pressure in live animals. EPR oxygen images show remarkable oxygen accuracy when combined with high precision and spatial resolution. Developing more effective means for obtaining SLR rates is of great practical, biological and medical importance. In this work we compared different pulse EPR imaging protocols and pulse sequences to establish ad...

  9. Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms.

    Directory of Open Access Journals (Sweden)

    Francesca Bertolini

    Full Text Available Few studies investigated the donkey (Equus asinus at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca. The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing and Ion Torrent (RRL runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources.

  10. Next Generation Semiconductor Based Sequencing of the Donkey (Equus asinus) Genome Provided Comparative Sequence Data against the Horse Genome and a Few Millions of Single Nucleotide Polymorphisms

    Science.gov (United States)

    Bertolini, Francesca; Scimone, Concetta; Geraci, Claudia; Schiavo, Giuseppina; Utzeri, Valerio Joe; Chiofalo, Vincenzo; Fontanesi, Luca

    2015-01-01

    Few studies investigated the donkey (Equus asinus) at the whole genome level so far. Here, we sequenced the genome of two male donkeys using a next generation semiconductor based sequencing platform (the Ion Proton sequencer) and compared obtained sequence information with the available donkey draft genome (and its Illumina reads from which it was originated) and with the EquCab2.0 assembly of the horse genome. Moreover, the Ion Torrent Personal Genome Analyzer was used to sequence reduced representation libraries (RRL) obtained from a DNA pool including donkeys of different breeds (Grigio Siciliano, Ragusano and Martina Franca). The number of next generation sequencing reads aligned with the EquCab2.0 horse genome was larger than those aligned with the draft donkey genome. This was due to the larger N50 for contigs and scaffolds of the horse genome. Nucleotide divergence between E. caballus and E. asinus was estimated to be ~ 0.52-0.57%. Regions with low nucleotide divergence were identified in several autosomal chromosomes and in the whole chromosome X. These regions might be evolutionally important in equids. Comparing Y-chromosome regions we identified variants that could be useful to track donkey paternal lineages. Moreover, about 4.8 million of single nucleotide polymorphisms (SNPs) in the donkey genome were identified and annotated combining sequencing data from Ion Proton (whole genome sequencing) and Ion Torrent (RRL) runs with Illumina reads. A higher density of SNPs was present in regions homologous to horse chromosome 12, in which several studies reported a high frequency of copy number variants. The SNPs we identified constitute a first resource useful to describe variability at the population genomic level in E. asinus and to establish monitoring systems for the conservation of donkey genetic resources. PMID:26151450

  11. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  12. Effects of Implantation Sequence on the Micro-defects in H and O Implanted Silicon

    Science.gov (United States)

    Wang, Zhuo; Yang, Lin; Zhang, Li-Zhu; Shi, Shao-Bo; Zhang, Peng; Cao, Xing-Zhong; Wang, Bao-Yi

    2016-06-01

    Cz n-type Si (100) wafers are implanted with 190 keV O and 40 keV H ions in different implantation sequences. Cross sectional transmission electron microscopy and slow positron annihilation spectroscopy are used to study the formation and evolution of micro-defects. Our results clearly show that the defect morphology depends strongly on the implantation sequence. Large cavities are observed in O preimplanted samples, while only platelets are observed in H preimplanted samples. The change regularity of the S parameter is the same for the Si samples co-implanted at different sequences. But in H preimplanted samples, the S parameter is a little higher. The effects of the implantation sequence on the micro-defects have been discussed in combination with H and O implantation-induced defects as well as their interactions upon annealing.

  13. Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources

    Science.gov (United States)

    Mizianty, Marcin J.; Stach, Wojciech; Chen, Ke; Kedarisetti, Kanaka Durga; Disfani, Fatemeh Miri; Kurgan, Lukasz

    2010-01-01

    Motivation: Intrinsically disordered proteins play a crucial role in numerous regulatory processes. Their abundance and ubiquity combined with a relatively low quantity of their annotations motivate research toward the development of computational models that predict disordered regions from protein sequences. Although the prediction quality of these methods continues to rise, novel and improved predictors are urgently needed. Results: We propose a novel method, named MFDp (Multilayered Fusion-based Disorder predictor), that aims to improve over the current disorder predictors. MFDp is as an ensemble of 3 Support Vector Machines specialized for the prediction of short, long and generic disordered regions. It combines three complementary disorder predictors, sequence, sequence profiles, predicted secondary structure, solvent accessibility, backbone dihedral torsion angles, residue flexibility and B-factors. Our method utilizes a custom-designed set of features that are based on raw predictions and aggregated raw values and recognizes various types of disorder. The MFDp is compared at the residue level on two datasets against eight recent disorder predictors and top-performing methods from the most recent CASP8 experiment. In spite of using training chains with ≤25% similarity to the test sequences, our method consistently and significantly outperforms the other methods based on the MCC index. The MFDp outperforms modern disorder predictors for the binary disorder assignment and provides competitive real-valued predictions. The MFDp's outputs are also shown to outperform the other methods in the identification of proteins with long disordered regions. Availability: http://biomine.ece.ualberta.ca/MFDp.html Supplementary information: Supplementary data are available at Bioinformatics online. Contact: lkurgan@ece.ualberta.ca PMID:20823312

  14. Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Schierup, M.H.; Jorgensen, F.G.;

    2005-01-01

    sequences (0.66X coverage) from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project") together with an initial evolutionary analysis. The non-repetitive fraction of the sequences was aligned to the UCSC human......Background: Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the artiodactyls. Results: We have generated similar to 3.84 million shotgun......-mouse alignment and the resulting three-species alignments were annotated using the human genome annotation. Ultra-conserved elements and miRNAs were identified. The results show that for each of these types of orthologous data, pig is much closer to human than mouse is. Purifying selection has been more...

  15. Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing

    Directory of Open Access Journals (Sweden)

    Li Wei

    2005-05-01

    Full Text Available Abstract Background Comparative whole genome analysis of Mammalia can benefit from the addition of more species. The pig is an obvious choice due to its economic and medical importance as well as its evolutionary position in the artiodactyls. Results We have generated ~3.84 million shotgun sequences (0.66X coverage from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project" together with an initial evolutionary analysis. The non-repetitive fraction of the sequences was aligned to the UCSC human-mouse alignment and the resulting three-species alignments were annotated using the human genome annotation. Ultra-conserved elements and miRNAs were identified. The results show that for each of these types of orthologous data, pig is much closer to human than mouse is. Purifying selection has been more efficient in pig compared to human, but not as efficient as in mouse, and pig seems to have an isochore structure most similar to the structure in human. Conclusion The addition of the pig to the set of species sequenced at low coverage adds to the understanding of selective pressures that have acted on the human genome by bisecting the evolutionary branch between human and mouse with the mouse branch being approximately 3 times as long as the human branch. Additionally, the joint alignment of the shot-gun sequences to the human-mouse alignment offers the investigator a rapid way to defining specific regions for analysis and resequencing.

  16. Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data

    Czech Academy of Sciences Publication Activity Database

    Macas, Jiří; Neumann, Pavel; Novák, Petr; Jiang, J.

    2010-01-01

    Roč. 26, č. 1797 (2010), s. 2101-2108. ISSN 1367-4803 R&D Projects: GA AV ČR KJB500960802; GA MŠk(CZ) OC10037; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50510513 Keywords : next-generation sequencing * satellite repeats * K-mer analysis Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.877, year: 2010

  17. A new proof for the convergence of an individual based model to the Trait substitution sequence

    CERN Document Server

    Gupta, Ankit; Tran, Viet Chi

    2012-01-01

    We consider a stochastic individual based model for a population structured by a vector trait and with logistic interactions. We consider its limit in a context from adaptive dynamics: the population is large, the mutations are rare and we view the process in the timescale of mutations. Using averaging techniques due to Kurtz (1992), we give a new proof of the convergence of the individual based model to the Trait substitution sequence of Metz et al. (1992) and rigorously proved by Champagnat (2006): assuming that "invasion implies fixation", we obtain in the limit a process that jumps from one population equilibrum to another one when mutations occur and invade the population.

  18. Estimation of physiological parameters using knowledge-based factor analysis of dynamic nuclear medicine image sequences

    International Nuclear Information System (INIS)

    The authors have previously developed a knowledge-based method of factor analysis to analyze dynamic nuclear medicine image sequences. In this paper, the authors analyze dynamic PET cerebral glucose metabolism and neuroreceptor binding studies. These methods have shown the ability to reduce the dimensionality of the data, enhance the image quality of the sequence, and generate meaningful functional images and their corresponding physiological time functions. The new information produced by the factor analysis has now been used to improve the estimation of various physiological parameters. A principal component analysis (PCA) is first performed to identify statistically significant temporal variations and remove the uncorrelated variations (noise) due to Poisson counting statistics. The statistically significant principal components are then used to reconstruct a noise-reduced image sequence as well as provide an initial solution for the factor analysis. Prior knowledge such as the compartmental models or the requirement of positivity and simple structure can be used to constrain the analysis. These constraints are used to rotate the factors to the most physically and physiologically realistic solution. The final result is a small number of time functions (factors) representing the underlying physiological processes and their associated weighting images representing the spatial localization of these functions. Estimation of physiological parameters can then be performed using the noise-reduced image sequence generated from the statistically significant PCs and/or the final factor images and time functions. These results are compared to the parameter estimation using standard methods and the original raw image sequences. Graphical analysis was performed at the pixel level to generate comparable parametric images of the slope and intercept (influx constant and distribution volume)

  19. Molecular Characterization of Five Potyviruses Infecting Korean Sweet Potatoes Based on Analyses of Complete Genome Sequences

    Directory of Open Access Journals (Sweden)

    Hae-Ryun Kwak

    2015-12-01

    Full Text Available Sweet potatoes (Ipomea batatas L. are grown extensively, in tropical and temperate regions, and are important food crops worldwide. In Korea, potyviruses, including Sweet potato feathery mottle virus (SPFMV, Sweet potato virus C (SPVC, Sweet potato virus G (SPVG, Sweet potato virus 2 (SPV2, and Sweet potato latent virus (SPLV, have been detected in sweet potato fields at a high (~95% incidence. In the present work, complete genome sequences of 18 isolates, representing the five potyviruses mentioned above, were compared with previously reported genome sequences. The complete genomes consisted of 10,081 to 10,830 nucleotides, excluding the poly-A tails. Their genomic organizations were typical of the Potyvirus genus, including one target open reading frame coding for a putative polyprotein. Based on phylogenetic analyses and sequence comparisons, the Korean SPFMV isolates belonged to the strains RC and O with >98% nucleotide sequence identity. Korean SPVC isolates had 99% identity to the Japanese isolate SPVC-Bungo and 70% identity to the SPFMV isolates. The Korean SPVG isolates showed 99% identity to the three previously reported SPVG isolates. Korean SPV2 isolates had 97% identity to the SPV2 GWB-2 isolate from the USA. Korean SPLV isolates had a relatively low (88% nucleotide sequence identity with the Taiwanese SPLV-TW isolates, and they were phylogenetically distantly related to SPFMV isolates. Recombination analysis revealed that possible recombination events occurred in the P1, HC-Pro and NIa-NIb regions of SPFMV and SPLV isolates and these regions were identified as hotspots for recombination in the sweet potato potyviruses.

  20. High resolution profiling of human exon methylation by liquid hybridization capture-based bisulfite sequencing

    Directory of Open Access Journals (Sweden)

    Wang Junwen

    2011-12-01

    Full Text Available Abstract Background DNA methylation plays important roles in gene regulation during both normal developmental and disease states. In the past decade, a number of methods have been developed and applied to characterize the genome-wide distribution of DNA methylation. Most of these methods endeavored to screen whole genome and turned to be enormously costly and time consuming for studies of the complex mammalian genome. Thus, they are not practical for researchers to study multiple clinical samples in biomarker research. Results Here, we display a novel strategy that relies on the selective capture of target regions by liquid hybridization followed by bisulfite conversion and deep sequencing, which is referred to as liquid hybridization capture-based bisulfite sequencing (LHC-BS. To estimate this method, we utilized about 2 μg of native genomic DNA from YanHuang (YH whole blood samples and a mature dendritic cell (mDC line, respectively, to evaluate their methylation statuses of target regions of exome. The results indicated that the LHC-BS system was able to cover more than 97% of the exome regions and detect their methylation statuses with acceptable allele dropouts. Most of the regions that couldn't provide accurate methylation information were distributed in chromosomes 6 and Y because of multiple mapping to those regions. The accuracy of this strategy was evaluated by pair-wise comparisons using the results from whole genome bisulfite sequencing and validated by bisulfite specific PCR sequencing. Conclusions In the present study, we employed a liquid hybridisation capture system to enrich for exon regions and then combined with bisulfite sequencing to examine the methylation statuses for the first time. This technique is highly sensitive and flexible and can be applied to identify differentially methylated regions (DMRs at specific genomic locations of interest, such as regulatory elements or promoters.

  1. A sequence-based genetic linkage map as a reference for Brassica rapa pseudochromosome assembly

    Directory of Open Access Journals (Sweden)

    Cheng Feng

    2011-05-01

    Full Text Available Abstract Background Brassica rapa is an economically important crop and a model plant for studies concerning polyploidization and the evolution of extreme morphology. The multinational B. rapa Genome Sequencing Project (BrGSP was launched in 2003. In 2008, next generation sequencing technology was used to sequence the B. rapa genome. Several maps concerning B. rapa pseudochromosome assembly have been published but their coverage of the genome is incomplete, anchoring approximately 73.6% of the scaffolds on to chromosomes. Therefore, a new genetic map to aid pseudochromosome assembly is required. Results This study concerns the construction of a reference genetic linkage map for Brassica rapa, forming the backbone for anchoring sequence scaffolds of the B. rapa genome resulting from recent sequencing efforts. One hundred and nineteen doubled haploid (DH lines derived from microspore cultures of an F1 cross between a Chinese cabbage (B. rapa ssp. pekinensis DH line (Z16 and a rapid cycling inbred line (L144 were used to construct the linkage map. PCR-based insertion/deletion (InDel markers were developed by re-sequencing the two parental lines. The map comprises a total of 507 markers including 415 InDels and 92 SSRs. Alignment and orientation using SSR markers in common with existing B. rapa linkage maps allowed ten linkage groups to be identified, designated A01-A10. The total length of the linkage map was 1234.2 cM, with an average distance of 2.43 cM between adjacent marker loci. The lengths of linkage groups ranged from 71.5 cM to 188.5 cM for A08 and A09, respectively. Using the developed linkage map, 152 scaffolds were anchored on to the chromosomes, encompassing more than 82.9% of the B. rapa genome. Taken together with the previously available linkage maps, 183 scaffolds were anchored on to the chromosomes and the total coverage of the genome was 88.9%. Conclusions The development of this linkage map is vital for the integration of genome

  2. Taxonomically Clustering Organisms Based on the Profiles of Gene Sequences Using PCA

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    E. Ramaraj

    2006-01-01

    Full Text Available The biological implications of bioinformatics can already be seen in various implementations. Biological taxonomy may seem like a simple science in which the biologists merely observe similarities among organisms and construct classifications according to those similarities[1], but it is not so simple. By applying data mining techniques on gene sequence database we can cluster the data to find interesting similarities in the gene expression data. One of the applications of such kind of clustering is taxonomically clustering the organisms based on their gene sequential expressions. In this study we outlined a method for taxonomical clustering of species of the organisms based on the genetic profile using Principal Component Analysis and Self Organizing Neural Networks. We have implemented the idea using Matlab and tried to cluster the gene sequences taken from PAUP version of the ML5/ML6 database. The taxa used for some of the basidiomycetous fungi form the database. To study the scalability issues another large gene sequence database was used. The proposed method clustered the species of organisms correctly in almost all the cases. The obtained were more significant and promising. The proposed method clustered the species of organisms correctly in almost all the cases. The obtained results were more significant and promising.

  3. Small RNA Sequencing Based Identification of MiRNAs in Daphnia magna.

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    Ercan Selçuk Ünlü

    Full Text Available Small RNA molecules are short, non-coding RNAs identified for their crucial role in post-transcriptional regulation. A well-studied example includes miRNAs (microRNAs which have been identified in several model organisms including the freshwater flea and planktonic crustacean Daphnia. A model for epigenetic-based studies with an available genome database, the identification of miRNAs and their potential role in regulating Daphnia gene expression has only recently garnered interest. Computational-based work using Daphnia pulex, has indicated the existence of 45 miRNAs, 14 of which have been experimentally verified. To extend this study, we took a sequencing approach towards identifying miRNAs present in a small RNA library isolated from Daphnia magna. Using Perl codes designed for comparative genomic analysis, 815,699 reads were obtained from 4 million raw reads and run against a database file of known miRNA sequences. Using this approach, we have identified 205 putative mature miRNA sequences belonging to 188 distinct miRNA families. Data from this study provides critical information necessary to begin an investigation into a role for these transcripts in the epigenetic regulation of Daphnia magna.

  4. A Chaos-Based Secure Direct-Sequence/Spread-Spectrum Communication System

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    Nguyen Xuan Quyen

    2013-01-01

    Full Text Available This paper proposes a chaos-based secure direct-sequence/spread-spectrum (DS/SS communication system which is based on a novel combination of the conventional DS/SS and chaos techniques. In the proposed system, bit duration is varied according to a chaotic behavior but is always equal to a multiple of the fixed chip duration in the communication process. Data bits with variable duration are spectrum-spread by multiplying directly with a pseudonoise (PN sequence and then modulated onto a sinusoidal carrier by means of binary phase-shift keying (BPSK. To recover exactly the data bits, the receiver needs an identical regeneration of not only the PN sequence but also the chaotic behavior, and hence data security is improved significantly. Structure and operation of the proposed system are analyzed in detail. Theoretical evaluation of bit-error rate (BER performance in presence of additive white Gaussian noise (AWGN is provided. Parameter choice for different cases of simulation is also considered. Simulation and theoretical results are shown to verify the reliability and feasibility of the proposed system. Security of the proposed system is also discussed.

  5. Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

    Science.gov (United States)

    Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

    2012-09-01

    Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. PMID:22676903

  6. Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes.

    Science.gov (United States)

    Ruppitsch, Werner; Pietzka, Ariane; Prior, Karola; Bletz, Stefan; Fernandez, Haizpea Lasa; Allerberger, Franz; Harmsen, Dag; Mellmann, Alexander

    2015-09-01

    Whole-genome sequencing (WGS) has emerged today as an ultimate typing tool to characterize Listeria monocytogenes outbreaks. However, data analysis and interlaboratory comparability of WGS data are still challenging for most public health laboratories. Therefore, we have developed and evaluated a new L. monocytogenes typing scheme based on genome-wide gene-by-gene comparisons (core genome multilocus the sequence typing [cgMLST]) to allow for a unique typing nomenclature. Initially, we determined the breadth of the L. monocytogenes population based on MLST data with a Bayesian approach. Based on the genome sequence data of representative isolates for the whole population, cgMLST target genes were defined and reappraised with 67 L. monocytogenes isolates from two outbreaks and serotype reference strains. The Bayesian population analysis generated five L. monocytogenes groups. Using all available NCBI RefSeq genomes (n = 36) and six additionally sequenced strains, all genetic groups were covered. Pairwise comparisons of these 42 genome sequences resulted in 1,701 cgMLST targets present in all 42 genomes with 100% overlap and ≥90% sequence similarity. Overall, ≥99.1% of the cgMLST targets were present in 67 outbreak and serotype reference strains, underlining the representativeness of the cgMLST scheme. Moreover, cgMLST enabled clustering of outbreak isolates with ≤10 alleles difference and unambiguous separation from unrelated outgroup isolates. In conclusion, the novel cgMLST scheme not only improves outbreak investigations but also enables, due to the availability of the automatically curated cgMLST nomenclature, interlaboratory exchange of data that are crucial, especially for rapid responses during transsectorial outbreaks. PMID:26135865

  7. HLA polymorphisms in Cabo Verde and Guiné-Bissau inferred from sequence-based typing.

    Science.gov (United States)

    Spínola, Hélder; Bruges-Armas, Jácome; Middleton, Derek; Brehm, António

    2005-10-01

    Human leukocyte antigen (HLA)-A, -B, and -DRB1 polymorphisms were examined in the Cabo Verde and Guiné-Bissau populations. The data were obtained at high-resolution level, using sequence-based typing. The most frequent alleles in each locus was: A*020101 (16.7% in Guiné-Bissau and 13.5% in Cabo Verde), B*350101 (14.4% in Guiné-Bissau and 13.2% in Cabo Verde), DRB1*1304 (19.6% in Guiné-Bissau), and DRB1*1101 (10.1% in Cabo Verde). The predominant three loci haplotype in Guiné-Bissau was A*2301-B*1503-DRB1*1101 (4.6%) and in Cabo Verde was A*3002-B*350101-DRB1*1001 (2.8%), exclusive to northwestern islands (5.6%) and absent in Guiné-Bissau. The present study corroborates historic sources and other genetic studies that say Cabo Verde were populated not only by Africans but also by Europeans. Haplotypes and dendrogram analysis shows a Caucasian genetic influence in today's gene pool of Cabo Verdeans. Haplotypes and allele frequencies present a differential distribution between southeastern and northwestern Cabo Verde islands, which could be the result of different genetic influences, founder effect, or bottlenecks. Dendrograms and principal coordinates analysis show that Guineans are more similar to North Africans than other HLA-studied sub-Saharans, probably from ancient and recent genetic contacts with other peoples, namely East Africans. PMID:16386651

  8. Statistical framework for detection of genetically modified organisms based on Next Generation Sequencing.

    Science.gov (United States)

    Willems, Sander; Fraiture, Marie-Alice; Deforce, Dieter; De Keersmaecker, Sigrid C J; De Loose, Marc; Ruttink, Tom; Herman, Philippe; Van Nieuwerburgh, Filip; Roosens, Nancy

    2016-02-01

    Because the number and diversity of genetically modified (GM) crops has significantly increased, their analysis based on real-time PCR (qPCR) methods is becoming increasingly complex and laborious. While several pioneers already investigated Next Generation Sequencing (NGS) as an alternative to qPCR, its practical use has not been assessed for routine analysis. In this study a statistical framework was developed to predict the number of NGS reads needed to detect transgene sequences, to prove their integration into the host genome and to identify the specific transgene event in a sample with known composition. This framework was validated by applying it to experimental data from food matrices composed of pure GM rice, processed GM rice (noodles) or a 10% GM/non-GM rice mixture, revealing some influential factors. Finally, feasibility of NGS for routine analysis of GM crops was investigated by applying the framework to samples commonly encountered in routine analysis of GM crops. PMID:26304412

  9. Towards Engineered Processes for Sequencing-Based Analysis of Single Circulating Tumor Cells.

    Science.gov (United States)

    Adalsteinsson, Viktor A; Love, J Christopher

    2014-05-01

    Sequencing-based analysis of single circulating tumor cells (CTCs) has the potential to revolutionize our understanding of metastatic cancer and improve clinical care. Technologies exist to enrich, identify, recover, and sequence single cells, but to enable systematic routine analysis of single CTCs from a range of cancer patients, there is a need to establish processes that efficiently integrate these specific operations. Such engineered processes should address challenges associated with the yield and viability of enriched CTCs, the robust identification of candidate single CTCs with minimal degradation of DNA, the bias in whole-genome amplification, and the efficient handling of candidate single CTCs or their amplified DNA products. Advances in methods for single-cell analysis and nanoscale technologies suggest opportunities to overcome these challenges, and could create integrated platforms that perform several of the unit operations together. Ultimately, technologies should be selected or adapted for optimal performance and compatibility in an integrated process. PMID:24839591

  10. Development of polymorphic microsatellite markers based on expressed sequence tags in Populus cathayana (Salicaceae).

    Science.gov (United States)

    Tian, Z Z; Zhang, F Q; Cai, Z Y; Chen, S L

    2016-01-01

    Populus cathayana occupies a large area within the northern, central, and southwestern regions of China, and is considered to be an important reforestation species in western China. In order to investigate the population genetic structure of this species, 10 polymorphic microsatellite loci were identified based on expressed sequence tags from de novo sequencing on the Illumina HiSeq 2000 platform. All microsatellite primers were tested on 48 P. cathayana individuals from four locations on the Qinghai-Tibet Plateau. The observed heterozygosity ranged from 0.000 to 1.000, and the null-allele frequency ranged from 0.000 to 0.904. These microsatellite markers may be a useful tool in genetic studies on P. cathayana and closely related species. PMID:27525845

  11. Systematic position of Myrtama Ovcz. & Kinz. based on morphological and nrDNA ITS sequence evidence

    Institute of Scientific and Technical Information of China (English)

    ZHANG Daoyuan; ZHANG Yuan; GASKIN J. F.; CHEN Zhiduan

    2006-01-01

    Myrtama is a genus named from Myricaria elegans Royle in the 1970's in terms of its morphological peculiarities. The establishment of this genus and its systematic position have been disputed since its inception. ITS sequences from 10 species of Tamaricaceae are reported, and analyzed by PAUP 4.0b8 and Bayesian Inference to reconstruct the phylogenies. A single ITS tree is generated from maximum parsimony and MrBayes analyses, respectively. The molecular data set shows strong support for Tamarix and Myricaria as monophyletic genera,and Myrtama as a sister group to the genus Myricaria.Based on morphological differences, a single morphological tree is also generated, in which two major lineages existed but Myrtama is a sister group to Tamarix, rather than Myricaria. The evidence from DNA sequences and morphological characters supports that Myicaria elegans should be put into neither Myricaria nor Tamarix, but kept in its own monotypic genus.

  12. A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs

    Directory of Open Access Journals (Sweden)

    Seitzer Phillip

    2012-11-01

    Full Text Available Abstract Background Discovery of functionally significant short, statistically overrepresented subsequence patterns (motifs in a set of sequences is a challenging problem in bioinformatics. Oftentimes, not all sequences in the set contain a motif. These non-motif-containing sequences complicate the algorithmic discovery of motifs. Filtering the non-motif-containing sequences from the larger set of sequences while simultaneously determining the identity of the motif is, therefore, desirable and a non-trivial problem in motif discovery research. Results We describe MotifCatcher, a framework that extends the sensitivity of existing motif-finding tools by employing random sampling to effectively remove non-motif-containing sequences from the motif search. We developed two implementations of our algorithm; each built around a commonly used motif-finding tool, and applied our algorithm to three diverse chromatin immunoprecipitation (ChIP data sets. In each case, the motif finder with the MotifCatcher extension demonstrated improved sensitivity over the motif finder alone. Our approach organizes candidate functionally significant discovered motifs into a tree, which allowed us to make additional insights. In all cases, we were able to support our findings with experimental work from the literature. Conclusions Our framework demonstrates that additional processing at the sequence entry level can significantly improve the performance of existing motif-finding tools. For each biological data set tested, we were able to propose novel biological hypotheses supported by experimental work from the literature. Specifically, in Escherichia coli, we suggested binding site motifs for 6 non-traditional LexA protein binding sites; in Saccharomyces cerevisiae, we hypothesize 2 disparate mechanisms for novel binding sites of the Cse4p protein; and in Halobacterium sp. NRC-1, we discoverd subtle differences in a general transcription factor (GTF binding site motif

  13. Effect of actuation sequence on flow rates of peristaltic micropumps with PZT actuators.

    Science.gov (United States)

    Jang, Ling-Sheng; Shu, Kuan; Yu, Yung-Chiang; Li, Yuan-Jie; Chen, Chiun-Hsun

    2009-02-01

    Many biomedical applications require the administration of drugs at a precise and preferably programmable rate. The flow rate generated by the peristaltic micropumps used in such applications depends on the actuation sequence. Accordingly, the current study performs an analytical and experimental investigation to determine the correlation between the dynamic response of the diaphragms in the micropump and the actuation sequence. A simple analytical model of a peristaltic micropump is established to analyze the shift in the resonant frequency of the diaphragms caused by the viscous damping effect. The analytical results show that this damping effect increases as the oscillation frequency of the diaphragm increases. A peristaltic micropump with three piezoelectric actuators is fabricated on a silicon substrate and is actuated using 2-, 3-, 4- and 6-phase actuation sequences via a driving system comprising a microprocessor and a phase controller. A series of experiments is conducted using de-ionized water as the working fluid to determine the diaphragm displacement and the flow rates induced by each of the different actuation sequences under phase frequencies ranging from 50 Hz to 1 MHz. The results show that the damping effect of actuation sequences influences diaphragm resonant frequency, which in turn affects the profiles of flow rates. PMID:18821016

  14. TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors.

    Directory of Open Access Journals (Sweden)

    Johannes Eichner

    Full Text Available One of the key mechanisms of transcriptional control are the specific connections between transcription factors (TF and cis-regulatory elements in gene promoters. The elucidation of these specific protein-DNA interactions is crucial to gain insights into the complex regulatory mechanisms and networks underlying the adaptation of organisms to dynamically changing environmental conditions. As experimental techniques for determining TF binding sites are expensive and mostly performed for selected TFs only, accurate computational approaches are needed to analyze transcriptional regulation in eukaryotes on a genome-wide level. We implemented a four-step classification workflow which for a given protein sequence (1 discriminates TFs from other proteins, (2 determines the structural superclass of TFs, (3 identifies the DNA-binding domains of TFs and (4 predicts their cis-acting DNA motif. While existing tools were extended and adapted for performing the latter two prediction steps, the first two steps are based on a novel numeric sequence representation which allows for combining existing knowledge from a BLAST scan with robust machine learning-based classification. By evaluation on a set of experimentally confirmed TFs and non-TFs, we demonstrate that our new protein sequence representation facilitates more reliable identification and structural classification of TFs than previously proposed sequence-derived features. The algorithms underlying our proposed methodology are implemented in the two complementary tools TFpredict and SABINE. The online and stand-alone versions of TFpredict and SABINE are freely available to academics at http://www.cogsys.cs.uni-tuebingen.de/software/TFpredict/ and http://www.cogsys.cs.uni-tuebingen.de/software/SABINE/.

  15. Sequence-structure based phylogeny of GPCR Class A Rhodopsin receptors.

    Science.gov (United States)

    Kakarala, Kavita Kumari; Jamil, Kaiser

    2014-05-01

    Current methods of G protein coupled receptors (GPCRs) phylogenetic classification are sequence based and therefore inappropriate for highly divergent sequences, sharing low sequence identity. In this study, sequence structure profile based alignment generated by PROMALS3D was used to understand the GPCR Class A Rhodopsin superfamily evolution using the MEGA 5 software. Phylogenetic analysis included a combination of Neighbor-Joining method and Maximum Likelihood method, with 1000 bootstrap replicates. Our study was able to identify potential ligand association for Class A Orphans and putative/unclassified Class A receptors with no cognate ligand information: GPR21 and GPR52 with fatty acids; GPR75 with Neuropeptide Y; GPR82, GPR18, GPR141 with N-arachidonylglycine; GPR176 with Free fatty acids, GPR10 with Tachykinin & Neuropeptide Y; GPR85 with ATP, ADP & UDP glucose; GPR151 with Galanin; GPR153 and GPR162 with Adrenalin, Noradrenalin; GPR146, GPR139, GPR142 with Neuromedin, Ghrelin, Neuromedin U-25 & Thyrotropin-releasing hormone; GPR171 with ATP, ADP & UDP Glucose; GPR88, GPR135, GPR161, GPR101with 11-cis-retinal; GPR83 with Tackykinin; GPR148 with Prostanoids, GPR109b, GPR81, GPR31with ATP & UTP and GPR150 with GnRH I & GnRHII. Furthermore, we suggest that this study would prove useful in re-classification of receptors, selecting templates for homology modeling and identifying ligands which may show cross reactivity with other GPCRs as signaling via multiple ligands play a significant role in disease modulation. PMID:24503482

  16. Studies on structure-based sequence alignment and phylogenies of beta-lactamases.

    Science.gov (United States)

    Salahuddin, Parveen; Khan, Asad U

    2014-01-01

    The β-lactamases enzymes cleave the amide bond in β-lactam ring, rendering β-lactam antibiotics harmless to bacteria. In this communication we have studied structure-function relationship and phylogenies of class A, B and D beta-lactamases using structure-based sequence alignment and phylip programs respectively. The data of structure-based sequence alignment suggests that in different isolates of TEM-1, mutations did not occur at or near sequence motifs. Since deletions are reported to be lethal to structure and function of enzyme. Therefore, in these variants antibiotic hydrolysis profile and specificity will be affected. The alignment data of class A enzyme SHV-1, CTX-M-15, class D enzyme, OXA-10, and class B enzyme VIM-2 and SIM-1 show sequence motifs along with other part of polypeptide are essentially conserved. These results imply that conformations of betalactamases are close to native state and possess normal hydrolytic activities towards beta-lactam antibiotics. However, class B enzyme such as IMP-1 and NDM-1 are less conserved than other class A and D studied here because mutation and deletions occurred at critically important region such as active site. Therefore, the structure of these beta-lactamases will be altered and antibiotic hydrolysis profile will be affected. Phylogenetic studies suggest that class A and D beta-lactamases including TOHO-1 and OXA-10 respectively evolved by horizontal gene transfer (HGT) whereas other member of class A such as TEM-1 evolved by gene duplication mechanism. Taken together, these studies justify structure-function relationship of beta-lactamases and phylogenetic studies suggest these enzymes evolved by different mechanisms. PMID:24966539

  17. The Recipe for Protein Sequence-Based Function Prediction and Its Implementation in the ANNOTATOR Software Environment.

    Science.gov (United States)

    Eisenhaber, Birgit; Kuchibhatla, Durga; Sherman, Westley; Sirota, Fernanda L; Berezovsky, Igor N; Wong, Wing-Cheong; Eisenhaber, Frank

    2016-01-01

    As biomolecular sequencing is becoming the main technique in life sciences, functional interpretation of sequences in terms of biomolecular mechanisms with in silico approaches is getting increasingly significant. Function prediction tools are most powerful for protein-coding sequences; yet, the concepts and technologies used for this purpose are not well reflected in bioinformatics textbooks. Notably, protein sequences typically consist of globular domains and non-globular segments. The two types of regions require cardinally different approaches for function prediction. Whereas the former are classic targets for homology-inspired function transfer based on remnant, yet statistically significant sequence similarity to other, characterized sequences, the latter type of regions are characterized by compositional bias or simple, repetitive patterns and require lexical analysis and/or empirical sequence pattern-function correlations. The recipe for function prediction recommends first to find all types of non-globular segments and, then, to subject the remaining query sequence to sequence similarity searches. We provide an updated description of the ANNOTATOR software environment as an advanced example of a software platform that facilitates protein sequence-based function prediction. PMID:27115649

  18. Efficient Implementation of Complementary Golay Sequences for PAR Reduction and Forward Error Correction in OFDM-based WLAN systems

    OpenAIRE

    Gil-Jiménez, Víctor P.; Fernández-Getino García, María Julia; García-Armada, Ana; Sánchez-Fernández, Matilde

    2008-01-01

    In this paper the use of complementary Golay sequences (CGS) for peak-to-average power ratio (PAR) reduction and forward error correction (FEC) in an orthogonal frequency division multiplexing (OFDM)-based wireless local area network (WLAN) system is explored; performance is examined and complexity issues are analyzed. We study their PAR reduction performance depending on sequence lengths and we have found that, for the case that the number of sub-carriers differs from the sequence length, so...

  19. Influence of Single Base Change in Shine-Dalgarno Sequence on the Stability of B.Subtilis Plasmid PSM604

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    B.Subtilis expression plasmids generally require a stringent Shine-Dalgarno Sequence(SDS). Site-directed-mutagenesis was explored to change the Shine-Dalgarno Sequence from AAAAATGGGG (mutant type) to AAAAAGGGGG (wild type) in recombinant plasmid PSM604. The single base substitution made the plasmid with wild SDS unstable in structure and segregation. The interaction of SDS with subtilisin leader sequence of PSM604 might be responsible for the instability of plasmid.

  20. Phylogeny of different geographic populations Apis cerana in China based on mtDNA cyt b sequences

    OpenAIRE

    Gao, Peng-fei; Zhao, Hui-ting; ZHANG, Chun-xiang; Jiang, Yu-suo

    2008-01-01

    In order to provide the basic datum to protect and rationally develop the Apis cerana resources in china, phylogeny of different geographic populations Apis cerana in China was studied based on mtDNA Cytochrome b gene sequences. In this study, the partial sequences of mtDNA Cytochrome b gene of 21 colonies of Apis cerana collected from 10 provinces and the homologous sequences of Apis nigrocincta and Apis mellifera downloaded from GenBank were analyzed. Molecular phylogenetic trees were reco...

  1. Robust design of an optical router based on a tapered side-coupled integrated spaced sequence of optical resonators.

    Science.gov (United States)

    Bettotti, P; Mancinelli, M; Guider, R; Masi, M; Vanacharla, M Rao; Pavesi, L

    2011-04-15

    A novel (to our knowledge) scheme of an optical router/switch element, composed of a tapered side-coupled integrated spaced sequence of optical resonators, is proposed. It is based on a modified design of the ring sequence in which the resonance conditions are set by the single ring resonance and by the coherent feedback of the sequence of rings. This double condition yields robustness against fabrication defects, dense routing capability, and high switching efficiency. PMID:21499394

  2. Effects of the bleaching sequence on the optical brighteners action in eucalyptus kraft pulp

    Directory of Open Access Journals (Sweden)

    Mauro Manfredi

    2014-06-01

    Full Text Available During the bleaching process the pulp is treated with chemical reagents that can be retained in the pulp and interfere in the action of the optical brighteners. Different bleaching sequences can produce pulps at the same brightness but with different potential to whiteness increase when treated with optical brighteners. The objective of this study was to evaluate the influence of the bleaching sequence on the efficiency of disulphonated and tetrasulphonated optical brighteners. Eucalyptus kraft pulp was bleached using four different bleaching sequences. For each pulp three brightness targets were aimeds. For each bleaching sequence mathematical model was generated for predicting the final pulp whiteness according to the initial brightness and the optical brightener charge applied. The presence of organochlorine residues in the pulp reduced the effectiveness of the optical brighteners. Therefore, bleaching sequences that use low chlorine dioxide charge favors for greater gains in whiteness with the application of optical brighteners. The replacement of the final chlorine dioxide bleaching stage with a hydrogen peroxide one in the sequence increased the efficiency of the optical brightening agents.

  3. Implicit structured sequence learning: an fMRI study of the structural mere-exposure effect.

    Science.gov (United States)

    Folia, Vasiliki; Petersson, Karl Magnus

    2014-01-01

    In this event-related fMRI study we investigated the effect of 5 days of implicit acquisition on preference classification by means of an artificial grammar learning (AGL) paradigm based on the structural mere-exposure effect and preference classification using a simple right-linear unification grammar. This allowed us to investigate implicit AGL in a proper learning design by including baseline measurements prior to grammar exposure. After 5 days of implicit acquisition, the fMRI results showed activations in a network of brain regions including the inferior frontal (centered on BA 44/45) and the medial prefrontal regions (centered on BA 8/32). Importantly, and central to this study, the inclusion of a naive preference fMRI baseline measurement allowed us to conclude that these fMRI findings were the intrinsic outcomes of the learning process itself and not a reflection of a preexisting functionality recruited during classification, independent of acquisition. Support for the implicit nature of the knowledge utilized during preference classification on day 5 come from the fact that the basal ganglia, associated with implicit procedural learning, were activated during classification, while the medial temporal lobe system, associated with explicit declarative memory, was consistently deactivated. Thus, preference classification in combination with structural mere-exposure can be used to investigate structural sequence processing (syntax) in unsupervised AGL paradigms with proper learning designs. PMID:24550865

  4. Implicit Structured Sequence Learning: An FMRI Study of the Structural Mere-Exposure Effect

    Directory of Open Access Journals (Sweden)

    Vasiliki eFolia

    2014-02-01

    Full Text Available In this event-related FMRI study we investigated the effect of five days of implicit acquisition on preference classification by means of an artificial grammar learning (AGL paradigm based on the structural mere-exposure effect and preference classification using a simple right-linear unification grammar. This allowed us to investigate implicit AGL in a proper learning design by including baseline measurements prior to grammar exposure. After 5 days of implicit acquisition, the FMRI results showed activations in a network of brain regions including the inferior frontal (centered on BA 44/45 and the medial prefrontal regions (centered on BA 8/32. Importantly, and central to this study, the inclusion of a naive preference FMRI baseline measurement allowed us to conclude that these FMRI findings were the intrinsic outcomes of the learning process itself and not a reflection of a preexisting functionality recruited during classification, independent of acquisition. Support for the implicit nature of the knowledge utilized during preference classification on day 5 come from the fact that the basal ganglia, associated with implicit procedural learning, were activated during classification, while the medial temporal lobe system, associated with explicit declarative memory, was consistently deactivated. Thus, preference classification in combination with structural mere-exposure can be used to investigate structural sequence processing (syntax in unsupervised AGL paradigms with proper learning designs.

  5. Electromyographic Patterns during Golf Swing: Activation Sequence Profiling and Prediction of Shot Effectiveness.

    Science.gov (United States)

    Verikas, Antanas; Vaiciukynas, Evaldas; Gelzinis, Adas; Parker, James; Olsson, M Charlotte

    2016-01-01

    This study analyzes muscle activity, recorded in an eight-channel electromyographic (EMG) signal stream, during the golf swing using a 7-iron club and exploits information extracted from EMG dynamics to predict the success of the resulting shot. Muscles of the arm and shoulder on both the left and right sides, namely flexor carpi radialis, extensor digitorum communis, rhomboideus and trapezius, are considered for 15 golf players (∼5 shots each). The method using Gaussian filtering is outlined for EMG onset time estimation in each channel and activation sequence profiling. Shots of each player revealed a persistent pattern of muscle activation. Profiles were plotted and insights with respect to player effectiveness were provided. Inspection of EMG dynamics revealed a pair of highest peaks in each channel as the hallmark of golf swing, and a custom application of peak detection for automatic extraction of swing segment was introduced. Various EMG features, encompassing 22 feature sets, were constructed. Feature sets were used individually and also in decision-level fusion for the prediction of shot effectiveness. The prediction of the target attribute, such as club head speed or ball carry distance, was investigated using random forest as the learner in detection and regression tasks. Detection evaluates the personal effectiveness of a shot with respect to the player-specific average, whereas regression estimates the value of target attribute, using EMG features as predictors. Fusion after decision optimization provided the best results: the equal error rate in detection was 24.3% for the speed and 31.7% for the distance; the mean absolute percentage error in regression was 3.2% for the speed and 6.4% for the distance. Proposed EMG feature sets were found to be useful, especially when used in combination. Rankings of feature sets indicated statistics for muscle activity in both the left and right body sides, correlation-based analysis of EMG dynamics and features

  6. Electromyographic Patterns during Golf Swing: Activation Sequence Profiling and Prediction of Shot Effectiveness

    Directory of Open Access Journals (Sweden)

    Antanas Verikas

    2016-04-01

    Full Text Available This study analyzes muscle activity, recorded in an eight-channel electromyographic (EMG signal stream, during the golf swing using a 7-iron club and exploits information extracted from EMG dynamics to predict the success of the resulting shot. Muscles of the arm and shoulder on both the left and right sides, namely flexor carpi radialis, extensor digitorum communis, rhomboideus and trapezius, are considered for 15 golf players (∼5 shots each. The method using Gaussian filtering is outlined for EMG onset time estimation in each channel and activation sequence profiling. Shots of each player revealed a persistent pattern of muscle activation. Profiles were plotted and insights with respect to player effectiveness were provided. Inspection of EMG dynamics revealed a pair of highest peaks in each channel as the hallmark of golf swing, and a custom application of peak detection for automatic extraction of swing segment was introduced. Various EMG features, encompassing 22 feature sets, were constructed. Feature sets were used individually and also in decision-level fusion for the prediction of shot effectiveness. The prediction of the target attribute, such as club head speed or ball carry distance, was investigated using random forest as the learner in detection and regression tasks. Detection evaluates the personal effectiveness of a shot with respect to the player-specific average, whereas regression estimates the value of target attribute, using EMG features as predictors. Fusion after decision optimization provided the best results: the equal error rate in detection was 24.3% for the speed and 31.7% for the distance; the mean absolute percentage error in regression was 3.2% for the speed and 6.4% for the distance. Proposed EMG feature sets were found to be useful, especially when used in combination. Rankings of feature sets indicated statistics for muscle activity in both the left and right body sides, correlation-based analysis of EMG

  7. Thermoelectric effect and its dependence on molecular length and sequence in single DNA molecules

    OpenAIRE

    Li, Yueqi; Xiang, Limin; Palma, Julio L.; ASAI, Yoshihiro; Tao, Nongjian

    2016-01-01

    Studying the thermoelectric effect in DNA is important for unravelling charge transport mechanisms and for developing relevant applications of DNA molecules. Here we report a study of the thermoelectric effect in single DNA molecules. By varying the molecular length and sequence, we tune the charge transport in DNA to either a hopping- or tunnelling-dominated regimes. The thermoelectric effect is small and insensitive to the molecular length in the hopping regime. In contrast, the thermoelect...

  8. A Study on the Effect of Welding Sequence in Fabrication of Large Stiffened Plate Panels

    Institute of Scientific and Technical Information of China (English)

    Pankaj Biswas; D.Anil Kumar; N.R.Mandal; M.M.Mahapatra

    2011-01-01

    Welding sequence has a significant effect on distortion pattern of large orthogonally stiffened panels normally used in ships and offshore structures.These deformations adversely affect the subsequent fitup and alignment of the adjacent panels.It may also result in loss of structural integrity.These panels primarily suffer from angular and buckling distortions.The extent of distortion depends on several parameters such as welding speed,plate thickness,welding current,voltage,restraints applied to the job while welding,thermal history as well as sequence of welding.Numerical modeling of welding and experimental validation of the FE model has been carried out for estimation of thermal history and resulting distortions.In the present work an FE model has been developed for studying the effect of welding sequence on the distortion pattern and its magnitude in fabrication of orthogonally stiffened plate panels.

  9. Genomic clones of bovine parvovirus: Construction and effect of deletions and terminal sequence inversions on infectivity

    Energy Technology Data Exchange (ETDEWEB)

    Shull, B.C.; Chen, K.C.; Lederman, M.; Stout, E.R.; Bates, R.C. (Virginia Polytechnic Institute and State Univ., Blacksburg (USA))

    1988-02-01

    Genomic clones of the autonomous parvovirus bovine parvovirus (BPV) were constructed by blunt-end ligation of reannealed virion plus and minus DNA strands into the plasmid pUC8. These clones were stable during propagation in Escherichia coli JM107. All clones tested were found to be infectious by the criteria of plaque titer and progressive cytophathic effect after transfection into bovine fetal lung cells. Sequencing of the recombinant plasmids demonstrated that all of the BPV inserts had left-end (3{prime})-terminal deletions of up to 34 bases. Defective genomes could also be detected in the progeny DNA even though the infection was initiated with homogeneous, cloned DNA. Full-length genomic clones with 3{prime} flip and 3{prime} flop conformations were constructed and were found to have equal infectivity. Expression of capsid proteins from tranfected genomes was demonstrated by hemagglutination, indirect immunofluorescence, and immunoprecipitation of ({sup 35}S)methionine-labeled cell lysates. Use of appropriate antiserum for immunoprecipitation showed the synthesis of BPV capsid and noncapsid proteins after transfection. Independently, a series of genomic clones with increasingly larger 3{prime}-terminal deletions was prepared from separately subcloned 3{prime}-terminal fragments. Transfection of these clones into bovine fetal lung cells revealed that deletions of up to 34 bases at the 3{prime} end lowered but did not abolish infectivity, while deletions of greater than 52 bases were lethal. End-label analysis showed that the 34-base deletion was repaired to wild-type length in the progeny virus.

  10. Automatic Tracing and Segmentation of Rat Mammary Fat Pads in MRI Image Sequences Based on Cartoon-Texture Model

    Institute of Scientific and Technical Information of China (English)

    TU Shengxian; ZHANG Su; CHEN Yazhu; Freedman Matthew T; WANG Bin; XUAN Jason; WANG Yue

    2009-01-01

    The growth patterns of mammary fat pads and glandular tissues inside the fat pads may be related with the risk factors of breast cancer.Quantitative measurements of this relationship are available after segmentation of mammary pads and glandular tissues.Rat fat pads may lose continuity along image sequences or adjoin similar intensity areas like epidermis and subcutaneous regions.A new approach for automatic tracing and segmentation of fat pads in magnetic resonance imaging (MRI) image sequences is presented,which does not require that the number of pads be constant or the spatial location of pads be adjacent among image slices.First,each image is decomposed into cartoon image and texture image based on cartoon-texture model.They will be used as smooth image and feature image for segmentation and for targeting pad seeds,respectively.Then,two-phase direct energy segmentation based on Chan-Vese active contour model is applied to partitioning the cartoon image into a set of regions,from which the pad boundary is traced iteratively from the pad seed.A tracing algorithm based on scanning order is proposed to accurately trace the pad boundary,which effectively removes the epidermis attached to the pad without any post processing as well as solves the problem of over-segmentation of some small holes inside the pad.The experimental results demonstrate the utility of this approach in accurate delineation of various numbers of mammary pads from several sets of MRI images.

  11. Thermoelectric effect and its dependence on molecular length and sequence in single DNA molecules

    Science.gov (United States)

    Li, Yueqi; Xiang, Limin; Palma, Julio L.; Asai, Yoshihiro; Tao, Nongjian

    2016-04-01

    Studying the thermoelectric effect in DNA is important for unravelling charge transport mechanisms and for developing relevant applications of DNA molecules. Here we report a study of the thermoelectric effect in single DNA molecules. By varying the molecular length and sequence, we tune the charge transport in DNA to either a hopping- or tunnelling-dominated regimes. The thermoelectric effect is small and insensitive to the molecular length in the hopping regime. In contrast, the thermoelectric effect is large and sensitive to the length in the tunnelling regime. These findings indicate that one may control the thermoelectric effect in DNA by varying its sequence and length. We describe the experimental results in terms of hopping and tunnelling charge transport models.

  12. Molecular phylogenetic relationships of China Seas groupers based on cytochrome b gene fragment sequences

    Institute of Scientific and Technical Information of China (English)

    DING Shaoxiong; ZHUANG Xuan; GUO Feng; WANG Jun; SU Yongquan; ZHANG Qiyong; LI Qifu

    2006-01-01

    The classification and evolutionary relationships are important issues in the study of the groupers. Cytochrome b gene fragment of twenty-eight grouper species within six genera of subfamily Epinephelinae was amplified using PCR techniques and the sequences were analyzed to derive the phylogenetic relationships of the groupers from the China Seas. Genetic information indexes, including Kimura-2 parameter genetic distance and Ts/Tv ratios, were generated by using a variety of biology softwares. With Niphon spinosus, Pagrus major and Pagrus auriga as the designated outgroups, phylogenetic trees, which invoke additional homologous sequences of other Epinephelus fishes from GenBank, were constructed based on the neighbor-joining (NJ), maximum-parsimony (MP), maximum-likelihood (ML) and minimum-evolution (ME) methods. Several conclusions were drawn from the DNA sequences analysis: (1) genus Plectropomus, which was early diverged, is the most primitive group in the subfamily Epinephelinae; (2) genus Variola is more closely related to genus Cephalopolis than the other four genera; (3) genus Cephalopolis is a monophyletic group and more primitive than genus Epinephelus; (4) Promicrops lanceolatus and Cromileptes altivelis should be included in genus Epinephelus; (5) there exist two sister groups in genus Epinephelus.

  13. Brain Bases of Working Memory for Time Intervals in Rhythmic Sequences.

    Science.gov (United States)

    Teki, Sundeep; Griffiths, Timothy D

    2016-01-01

    Perception of auditory time intervals is critical for accurate comprehension of natural sounds like speech and music. However, the neural substrates and mechanisms underlying the representation of time intervals in working memory are poorly understood. In this study, we investigate the brain bases of working memory for time intervals in rhythmic sequences using functional magnetic resonance imaging. We used a novel behavioral paradigm to investigate time-interval representation in working memory as a function of the temporal jitter and memory load of the sequences containing those time intervals. Human participants were presented with a sequence of intervals and required to reproduce the duration of a particular probed interval. We found that perceptual timing areas including the cerebellum and the striatum were more or less active as a function of increasing and decreasing jitter of the intervals held in working memory respectively whilst the activity of the inferior parietal cortex is modulated as a function of memory load. Additionally, we also analyzed structural correlations between gray and white matter density and behavior and found significant correlations in the cerebellum and the striatum, mirroring the functional results. Our data demonstrate neural substrates of working memory for time intervals and suggest that the cerebellum and the striatum represent core areas for representing temporal information in working memory. PMID:27313506

  14. Brain bases of working memory for time intervals in rhythmic sequences

    Directory of Open Access Journals (Sweden)

    Sundeep eTeki

    2016-06-01

    Full Text Available Perception of auditory time intervals is critical for accurate comprehension of natural sounds like speech and music. However, the neural substrates and mechanisms underlying the representation of time intervals in working memory are poorly understood. In this study, we investigate the brain bases of working memory for time intervals in rhythmic sequences using functional magnetic resonance imaging.We used a novel behavioral paradigm to investigate time-interval representation in working memory as a function of the temporal jitter and memory load of the sequences containing those time intervals. Human participants were presented with a sequence of intervals and required to reproduce the duration of a particular probed interval. We found that perceptual timing areas including the cerebellum and the striatum were more or less active as a function of increasing and decreasing jitter of the intervals held in working memory respectively whilst the activity of the inferior parietal cortex is modulated as a function of memory load. Additionally, we also analyzed structural correlations between grey and white matter density and behavior and found significant correlations in the cerebellum and the striatum, mirroring the functional results.Our data demonstrate neural substrates of working memory for time intervals and suggest that the cerebellum and the striatum represent core areas for representing temporal information in working memory.

  15. Sonication-based isolation and enrichment of Chlorella protothecoides chloroplasts for illumina genome sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Angelova, Angelina [University of Arizona; Park, Sang-Hycuk [University of Arizona; Kyndt, John [Bellevue University; Fitzsimmons, Kevin [University of Arizona; Brown, Judith K [University of Arizona

    2013-09-01

    With the increasing world demand for biofuel, a number of oleaginous algal species are being considered as renewable sources of oil. Chlorella protothecoides Krüger synthesizes triacylglycerols (TAGs) as storage compounds that can be converted into renewable fuel utilizing an anabolic pathway that is poorly understood. The paucity of algal chloroplast genome sequences has been an important constraint to chloroplast transformation and for studying gene expression in TAGs pathways. In this study, the intact chloroplasts were released from algal cells using sonication followed by sucrose gradient centrifugation, resulting in a 2.36-fold enrichment of chloroplasts from C. protothecoides, based on qPCR analysis. The C. protothecoides chloroplast genome (cpDNA) was determined using the Illumina HiSeq 2000 sequencing platform and found to be 84,576 Kb in size (8.57 Kb) in size, with a GC content of 30.8 %. This is the first report of an optimized protocol that uses a sonication step, followed by sucrose gradient centrifugation, to release and enrich intact chloroplasts from a microalga (C. prototheocoides) of sufficient quality to permit chloroplast genome sequencing with high coverage, while minimizing nuclear genome contamination. The approach is expected to guide chloroplast isolation from other oleaginous algal species for a variety of uses that benefit from enrichment of chloroplasts, ranging from biochemical analysis to genomics studies.

  16. Innovative molecular diagnosis of Trichinella species based on β-carbonic anhydrase genomic sequence.

    Science.gov (United States)

    Zolfaghari Emameh, Reza; Kuuslahti, Marianne; Näreaho, Anu; Sukura, Antti; Parkkila, Seppo

    2016-03-01

    Trichinellosis is a helminthic infection where different species of Trichinella nematodes are the causative agents. Several molecular assays have been designed to aid diagnostics of trichinellosis. These assays are mostly complex and expensive. The genomes of Trichinella species contain certain parasite-specific genes, which can be detected by polymerase chain reaction (PCR) methods. We selected β-carbonic anhydrase (β-CA) gene as a target, because it is present in many parasites genomes but absent in vertebrates. We developed a novel β-CA gene-based method for detection of Trichinella larvae in biological samples. We first identified a β-CA protein sequence from Trichinella spiralis by bioinformatic tools using β-CAs from Caenorhabditis elegans and Drosophila melanogaster. Thereafter, 16 sets of designed primers were tested to detect β-CA genomic sequences from three species of Trichinella, including T. spiralis, Trichinella pseudospiralis and Trichinella nativa. Among all 16 sets of designed primers, the primer set No. 2 efficiently amplified β-CA genomic sequences from T. spiralis, T. pseudospiralis and T. nativa without any false-positive amplicons from other parasite samples including Toxoplasma gondii, Toxocara cati and Parascaris equorum. This robust and straightforward method could be useful for meat inspection in slaughterhouses, quality control by food authorities and medical laboratories. PMID:26639312

  17. The Teaching of Biochemistry: An Innovative Course Sequence Based on the Logic of Chemistry

    Science.gov (United States)

    Jakubowski, Henry V.; Owen, Whyte G.

    1998-06-01

    An innovative course sequence for the teaching of biochemistry is offered, which more truly reflects the common philosophy found in biochemistry texts: that the foundation of biological phenomena can best be understood through the logic of chemistry. Topic order is chosen to develop an emerging understanding that is based on chemical principles. Preeminent biological questions serve as a framework for the course. Lipid and lipid-aggregate structures are introduced first, since it is more logical to discuss the intermolecular association of simple amphiphiles to form micelle and bilayer formations than to discuss the complexities of protein structure/folding. Protein, nucleic acid, and carbohydrate structures are studied next. Binding, a noncovalent process and the simplest expression of macromolecular function, follows. The physical (noncovalent) transport of solute molecules across a biological membrane is studied next, followed by the chemical transformation of substrates by enzymes. These are logical extensions of the expression of molecular function, first involving a simpler (physical transport) and second, a more complex (covalent transformation) process. The final sequence involves energy and signal transduction. This unique course sequence emerges naturally when chemical logic is used as an organizing paradigm for structuring a biochemistry course. Traditional order, which seems to reflect historic trends in research, or even an order derived from the central dogma of biology can not provide this logical framework.

  18. Origin and relationships of Saintpaulia (Gesneriaceae) based on ribosomal DNA internal transcribed spacer (ITS) sequences.

    Science.gov (United States)

    Moller, M; Cronk, Q

    1997-07-01

    Phylogenetic relationships of eight species of Saintpaulia H. Wendl., 19 species of Streptocarpus Lindl. (representing all major growth forms within the genus), and two outgroups (Haberlea rhodopensis Friv., Chirita spadiciformis W. T. Wang) were examined using comparative nucleotide sequences from the two internal transcribed spacers (ITS) of nuclear ribosomal DNA. The length of the ITS 1 region ranged from 228 to 249 base pairs (bp) and the ITS 2 region from 196 to 245 bp. Pairwise sequence divergence across both spacers for ingroup and outgroup species ranged from 0 to 29%. Streptocarpus is not monophyletic, and Saintpaulia is nested within Streptocarpus subgenus Streptocarpella. Streptocarpus subgenus Streptocarpus is monophyletic. The ITS sequence data demonstrate that the unifoliate Streptocarpus species form a clade, and are also characterized by a unique 47-bp deletion in ITS 2. The results strongly support the monophyly of (1) Saintpaulia, and (2) Saintpaulia plus the African members of the subgenus Streptocarpella of Streptocarpus. The data suggest the evolution of Saintpaulia from Streptocarpus subgenus Streptocarpella. The differences in flower and vegetative characters are probably due to ecological adaptation leading to a relatively rapid radiation of Saintpaulia. PMID:21708650

  19. Clustering Protein Sequences Using Affinity Propagation Based on an Improved Similarity Measure

    Directory of Open Access Journals (Sweden)

    Fan Yang

    2010-01-01

    Full Text Available The sizes of the protein databases are growing rapidly nowadays, thus it becomes increasingly important to cluster protein sequences only based on sequence information. In this paper we improve the similarity measure proposed by Kelil et al, then cluster sequences using the Affinity propagation (AP algorithm and provide a method to decide the input preference of AP algorithm. We tested our method extensively and compared its performance with other four methods on several datasets of COG, G protein, CAZy, SCOP database. We consistently observed that, the number of clusters that we obtained for a given set of proteins approximate to the correct number of clusters in that set. Moreover, in our experiments, the quality of the clusters when quantified by F-measure was better than that of other algorithms (on average, it is 15% better than that of BlastClust, 56% better than that of TribeMCL, 23% better than that of CLUSS, and 42% better than that of Spectral clustering.

  20. Genotyping of B. licheniformis based on a novel multi-locus sequence typing (MLST scheme

    Directory of Open Access Journals (Sweden)

    Madslien Elisabeth H

    2012-10-01

    Full Text Available Abstract Background Bacillus licheniformis has for many years been used in the industrial production of enzymes, antibiotics and detergents. However, as a producer of dormant heat-resistant endospores B. licheniformis might contaminate semi-preserved foods. The aim of this study was to establish a robust and novel genotyping scheme for B. licheniformis in order to reveal the evolutionary history of 53 strains of this species. Furthermore, the genotyping scheme was also investigated for its use to detect food-contaminating strains. Results A multi-locus sequence typing (MLST scheme, based on the sequence of six house-keeping genes (adk, ccpA, recF, rpoB, spo0A and sucC of 53 B. licheniformis strains from different sources was established. The result of the MLST analysis supported previous findings of two different subgroups (lineages within this species, named “A” and “B” Statistical analysis of the MLST data indicated a higher rate of recombination within group “A”. Food isolates were widely dispersed in the MLST tree and could not be distinguished from the other strains. However, the food contaminating strain B. licheniformis NVH1032, represented by a unique sequence type (ST8, was distantly related to all other strains. Conclusions In this study, a novel and robust genotyping scheme for B. licheniformis was established, separating the species into two subgroups. This scheme could be used for further studies of evolution and population genetics in B. licheniformis.

  1. A reassessment of the evolutionary timescale of bat rabies viruses based upon glycoprotein gene sequences.

    Science.gov (United States)

    Kuzmina, Natalia A; Kuzmin, Ivan V; Ellison, James A; Taylor, Steven T; Bergman, David L; Dew, Beverly; Rupprecht, Charles E

    2013-10-01

    Rabies, an acute progressive encephalomyelitis caused by viruses in the genus Lyssavirus, is one of the oldest known infectious diseases. Although dogs and other carnivores represent the greatest threat to public health as rabies reservoirs, it is commonly accepted that bats are the primary evolutionary hosts of lyssaviruses. Despite early historical documentation of rabies, molecular clock analyses indicate a quite young age of lyssaviruses, which is confusing. For example, the results obtained for partial and complete nucleoprotein gene sequences of rabies viruses (RABV), or for a limited number of glycoprotein gene sequences, indicated that the time of the most recent common ancestor (TMRCA) for current bat RABV diversity in the Americas lies in the seventeenth to eighteenth centuries and might be directly or indirectly associated with the European colonization. Conversely, several other reports demonstrated high genetic similarity between lyssavirus isolates, including RABV, obtained within a time interval of 25-50 years. In the present study, we attempted to re-estimate the age of several North American bat RABV lineages based on the largest set of complete and partial glycoprotein gene sequences compiled to date (n = 201) employing a codon substitution model. Although our results overlap with previous estimates in marginal areas of the 95 % high probability density (HPD), they suggest a longer evolutionary history of American bat RABV lineages (TMRCA at least 732 years, with a 95 % HPD 436-1107 years). PMID:23839669

  2. A CLIQUE algorithm using DNA computing techniques based on closed-circle DNA sequences.

    Science.gov (United States)

    Zhang, Hongyan; Liu, Xiyu

    2011-07-01

    DNA computing has been applied in broad fields such as graph theory, finite state problems, and combinatorial problem. DNA computing approaches are more suitable used to solve many combinatorial problems because of the vast parallelism and high-density storage. The CLIQUE algorithm is one of the gird-based clustering techniques for spatial data. It is the combinatorial problem of the density cells. Therefore we utilize DNA computing using the closed-circle DNA sequences to execute the CLIQUE algorithm for the two-dimensional data. In our study, the process of clustering becomes a parallel bio-chemical reaction and the DNA sequences representing the marked cells can be combined to form a closed-circle DNA sequences. This strategy is a new application of DNA computing. Although the strategy is only for the two-dimensional data, it provides a new idea to consider the grids to be vertexes in a graph and transform the search problem into a combinatorial problem. PMID:21511001

  3. Nanopore Analysis of Nucleic Acids: Single-Molecule Studies of Molecular Dynamics, Structure, and Base Sequence

    Science.gov (United States)

    Olasagasti, Felix; Deamer, David W.

    Nucleic acids are linear polynucleotides in which each base is covalently linked to a pentose sugar and a phosphate group carrying a negative charge. If a pore having roughly the crosssectional diameter of a single-stranded nucleic acid is embedded in a thin membrane and a voltage of 100 mV or more is applied, individual nucleic acids in solution can be captured by the electrical field in the pore and translocated through by single-molecule electrophoresis. The dimensions of the pore cannot accommodate anything larger than a single strand, so each base in the molecule passes through the pore in strict linear sequence. The nucleic acid strand occupies a large fraction of the pore's volume during translocation and therefore produces a transient blockade of the ionic current created by the applied voltage. If it could be demonstrated that each nucleotide in the polymer produced a characteristic modulation of the ionic current during its passage through the nanopore, the sequence of current modulations would reflect the sequence of bases in the polymer. According to this basic concept, nanopores are analogous to a Coulter counter that detects nanoscopic molecules rather than microscopic [1,2]. However, the advantage of nanopores is that individual macromolecules can be characterized because different chemical and physical properties affect their passage through the pore. Because macromolecules can be captured in the pore as well as translocated, the nanopore can be used to detect individual functional complexes that form between a nucleic acid and an enzyme. No other technique has this capability.

  4. Automated family-based naming of small RNAs for next generation sequencing data using a modified MD5-digest algorithm

    OpenAIRE

    Liu, Guodong; Li, Zhihua; Lin, Yuefeng; John, Bino

    2012-01-01

    We developed NameMyGene, a web tool and a stand alone program to easily generate putative family-based names for small RNA sequences so that laboratories can easily organize, analyze, and observe patterns from, the massive amount of data generated by next-generation sequencers. NameMyGene, also applicable to other emerging methods such as RNA-Seq, and Chip-Seq, solely uses the input small RNA sequence and does not require any additional data such as other sequence data sets. The web server an...

  5. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

    Directory of Open Access Journals (Sweden)

    Wan-Ping Lee

    Full Text Available MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me.

  6. Long-term tillage and cropping sequence effects on dryland residue and soil carbon fractions

    Science.gov (United States)

    Dryland soil N conservation and mineralization as influenced by long-term management practices is needed to reduce N fertilization rate, N leaching, and N2O (a greenhouse gas) emission. We evaluated the 21-yr effects of combinations of tillage and cropping sequences on dryland crop biomass (stems + ...

  7. Effects of Representation Sequences and Spatial Ability on Students' Scientific Understandings about the Mechanism of Breathing

    Science.gov (United States)

    Wu, Hsin-Kai; Lin, Yu-Fen; Hsu, Ying-Shao

    2013-01-01

    The purpose of this study was to investigate the effects of representation sequences and spatial ability on students' scientific understandings about the mechanism of breathing in human beings. 130 seventh graders were assigned to two groups with different sequential combinations of static and dynamic representations: SD group (i.e., viewing…

  8. Archaeorhizomyces borealis sp. nov. and a sequence-based classification of related soil fungal species.

    Science.gov (United States)

    Menkis, Audrius; Urbina, Hector; James, Timothy Y; Rosling, Anna

    2014-12-01

    The class Archaeorhizomycetes (Taphrinomycotina, Ascomycota) was introduced to accommodate an ancient lineage of soil-inhabiting fungi found in association with plant roots. Based on environmental sequencing data Archaeorhizomycetes may comprise a significant proportion of the total fungal community in soils. Yet the only species described and cultivated in this class is Archaeorhizomyces finlayi. In this paper, we describe a second species from a pure culture, Archaeorhizomyces borealis NS99-600(T) (=CBS138755(ExT)) based on morphological, physiological, and multi-locus molecular characterization. Archaeorhizomyces borealis was isolated from a root tip of a Pinus sylvestris seedling grown in a forest nursery in Lithuania. Analysis of Archaeorhizomycete species from environmental samples shows that it has a Eurasian distribution and is the most commonly observed species. Archaeorhizomyces borealis shows slow growth in culture and forms yellowish creamy colonies, characteristics that distinguish A. borealis from its closest relative A. finlayi. Here we also propose a sequence-based taxonomic classification of Archaeorhizomycetes and predict that approximately 500 species in this class remain to be isolated and described. PMID:25457942

  9. Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences

    Directory of Open Access Journals (Sweden)

    Michelle Klein Sercundes

    2016-03-01

    Full Text Available Abstract Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC and beta subunit of RNA polymerase (rpoB, and mitochondrial gene coding for cytochrome B (cytB were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG, Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genusHammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well.

  10. Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences.

    Science.gov (United States)

    Sercundes, Michelle Klein; Valadas, Samantha Yuri Oshiro Branco; Keid, Lara Borges; Oliveira, Tricia Maria Ferreira Souza; Ferreira, Helena Lage; Vitor, Ricardo Wagner de Almeida; Gregori, Fábio; Soares, Rodrigo Martins

    2016-01-01

    Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC) and beta subunit of RNA polymerase (rpoB), and mitochondrial gene coding for cytochrome B (cytB) were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG), Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genus Hammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well. PMID:27007245

  11. Aviram-Ratner rectifying mechanism for DNA base-pair sequencing through graphene nanogaps

    Science.gov (United States)

    Agapito, Luis A.; Gayles, Jacob; Wolowiec, Christian; Kioussis, Nicholas

    2012-04-01

    We demonstrate that biological molecules such as Watson-Crick DNA base pairs can behave as biological Aviram-Ratner electrical rectifiers because of the spatial separation and weak hydrogen bonding between the nucleobases. We have performed a parallel computational implementation of the ab initio non-equilibrium Green’s function (NEGF) theory to determine the electrical response of graphene—base-pair—graphene junctions. The results show an asymmetric (rectifying) current-voltage response for the cytosine-guanine base pair adsorbed on a graphene nanogap. In sharp contrast we find a symmetric response for the thymine-adenine case. We propose applying the asymmetry of the current-voltage response as a sensing criterion to the technological challenge of rapid DNA sequencing via graphene nanogaps.

  12. Next Generation Sequencing-Based Analysis of Repetitive DNA in the Model Dioceous Plant Silene latifolia

    Czech Academy of Sciences Publication Activity Database

    Macas, Jiří; Kejnovský, Eduard; Neumann, Pavel; Novák, Petr; Koblížková, Andrea; Vyskot, Boris

    2011-01-01

    Roč. 6, č. 11 (2011), e27335. E-ISSN 1932-6203 R&D Projects: GA MŠk(CZ) OC10037; GA MŠk(CZ) LC06004; GA MŠk(CZ) LH11058; GA ČR(CZ) GAP501/10/0102; GA ČR(CZ) GAP305/10/0930 Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z50040702 Keywords : Plant genome * Sequencing-Based Analyses * Repetitive DNA * Silene latifolia Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.092, year: 2011

  13. Fast and Reliable PCA-Based Temporal Segmentation of Video Sequences

    Czech Academy of Sciences Publication Activity Database

    Filip, Jiří; Haindl, Michal

    Los Alamitos: IEEE Press, 2008, s. 1-4. ISBN 978-1-4244-2174-9. [19th International Conference on Pattern Recognition. Tampa (US), 07.12.2008-11.12.2008] R&D Projects: GA AV ČR 1ET400750407; GA ČR GA102/08/0593 Grant ostatní: GA MŠk(CZ) 2C06019; Commision EU(XE) 41358 Institutional research plan: CEZ:AV0Z10750506 Keywords : video segmentation Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2008/RO/filip-fast and reliable pca-based temporal segmentation of video sequences.pdf

  14. A sequence-based dynamic ensemble learning system for protein ligand-binding site prediction

    KAUST Repository

    Chen, Peng

    2015-12-03

    Background: Proteins have the fundamental ability to selectively bind to other molecules and perform specific functions through such interactions, such as protein-ligand binding. Accurate prediction of protein residues that physically bind to ligands is important for drug design and protein docking studies. Most of the successful protein-ligand binding predictions were based on known structures. However, structural information is not largely available in practice due to the huge gap between the number of known protein sequences and that of experimentally solved structures

  15. Deep sequencing-based transcriptome analysis of Plutella xylostella larvae parasitized by Diadegma semiclausum

    Directory of Open Access Journals (Sweden)

    Glatz Richard V

    2011-09-01

    Full Text Available Abstract Background Parasitoid insects manipulate their hosts' physiology by injecting various factors into their host upon parasitization. Transcriptomic approaches provide a powerful approach to study insect host-parasitoid interactions at the molecular level. In order to investigate the effects of parasitization by an ichneumonid wasp (Diadegma semiclausum on the host (Plutella xylostella, the larval transcriptome profile was analyzed using a short-read deep sequencing method (Illumina. Symbiotic polydnaviruses (PDVs associated with ichneumonid parasitoids, known as ichnoviruses, play significant roles in host immune suppression and developmental regulation. In the current study, D. semiclausum ichnovirus (DsIV genes expressed in P. xylostella were identified and their sequences compared with other reported PDVs. Five of these genes encode proteins of unknown identity, that have not previously been reported. Results De novo assembly of cDNA sequence data generated 172,660 contigs between 100 and 10000 bp in length; with 35% of > 200 bp in length. Parasitization had significant impacts on expression levels of 928 identified insect host transcripts. Gene ontology data illustrated that the majority of the differentially expressed genes are involved in binding, catalytic activity, and metabolic and cellular processes. In addition, the results show that transcription levels of antimicrobial peptides, such as gloverin, cecropin E and lysozyme, were up-regulated after parasitism. Expression of ichnovirus genes were detected in parasitized larvae with 19 unique sequences identified from five PDV gene families including vankyrin, viral innexin, repeat elements, a cysteine-rich motif, and polar residue rich protein. Vankyrin 1 and repeat element 1 genes showed the highest transcription levels among the DsIV genes. Conclusion This study provides detailed information on differential expression of P. xylostella larval genes following parasitization, Ds

  16. Molecular identification based on ITS sequences for Kappaphycus and Eucheuma cultivated in China

    Institute of Scientific and Technical Information of China (English)

    ZHAO Sufen; HE Peimin

    2011-01-01

    The systematic classification of the Eucheurnatoideae is difficult because of their variable morphology and interpretation of reproductive structures.Kappaphycus and Eucheuma specimens cultivated on the Hainan and Fujian coast of China were introduced from Vietnam,the Philippines and Indonesia.Combined with morphological characteristics,all Kappaphycus and Eucheuma cultivated strains were identified by internal transcribed spacer (ITS) sequences.The phylogenetic tree was constructed using neighbor-joining and maximum likelihood methods.The results indicate that different ITS sequence lengths occurred in the different genera and species.An obvious difference in morphology could be found in the protuberance shape between Kappaphycus and Eucheuma.The protuberance in Eucheuma was thorn-like and in Kappaphycus was wartlike or papillate.Their ITS sequence lengths differed significantly in nucleotide variation rates up to 58.55%-63.90%.All nucleotide variations occurred in the ITS1 andITS2 regions except for five nucleotide transversions in the 5.8S rDNA region.In addition,the difference was at the branches among congeneric species.Kappaphycus sp.had branches with small buds,while K.alvarezii did not have such a feature.The nucleotide variation rates varied from 7.02% to 7.48% among species; within the same species of the clades it was <1.20%.Eucheumatoideae algae cultivated in China consisted of three clades,K.alvarezii,Kappaphycus sp.,and E.denticulatum.The results indicate that ITS sequence analysis was an effective way for identification of interspecies and intraspecies phylogenetic relationships and might provide a clue for molecular identification of algal Eucheumatoideae.

  17. Sequence Effect on the Topology of 3 + 1 Interlocked Bimolecular DNA G-Quadruplexes.

    Science.gov (United States)

    Gao, Shang; Cao, Yanwei; Yan, Yuting; Guo, Xinhua

    2016-05-17

    Electrospray ionization mass spectrometry (ESI-MS) combined with fluorescence, circular dichroism, UV spectrophotometer, and native polyacrylamide gel electrophoresis techniques are used to study structural features of interlocked dimers formed by DNA sequence 93del (GGGGTGGGAGGAGGGT) and its derivatives. Herein, we demonstrate that the interlocked dimers can be distinguished from stacked dimers formed by sequences T30923 (GGGTGGGTGGGTGGGT) and T30177 (GTGGTGGGTGGGTGGGT). In addition, loop length, the base at 5'-end, and the isolation of T and TT to the first 4G tract do significantly influence the formation and topologies of interlocked dimers. Furthermore, our results suggest that the 4G tract and the 2G tract in various locations in the 93del derivative sequence can form interlocked structure. This work not only provides new insight into the assembly of 3 + 1 interlocked DNA conformations but also demonstrates that ESI-MS combined with other analytical methods is rapid and useful for DNA structural studies. PMID:27027538

  18. Effect of sequence-dependent rigidity on plectoneme localization in dsDNA

    Science.gov (United States)

    Medalion, Shlomi; Rabin, Yitzhak

    2016-04-01

    We use Monte-Carlo simulations to study the effect of variable rigidity on plectoneme formation and localization in supercoiled double-stranded DNA. We show that the presence of soft sequences increases the number of plectoneme branches and that the edges of the branches tend to be localized at these sequences. We propose an experimental approach to test our results in vitro, and discuss the possible role played by plectoneme localization in the search process of transcription factors for their targets (promoter regions) on the bacterial genome.

  19. Going, going, gone: characterizing the time-course of congruency sequence effects

    Directory of Open Access Journals (Sweden)

    TobiasEgner

    2010-09-01

    Full Text Available Performance on traditional selective attention tasks, like the Stroop and flanker protocols, is subject to modulation by trial history, whereby the magnitude of congruency (or conflict effects is often found to decrease following an incongruent trial compared to a congruent one. These ‘congruency sequence effects’ (CSEs typically appear to reflect a mesh of memory- and attention-based processes. The current study aimed to shed new light on the nature of the attention-based contribution to CSEs, by characterizing the shape of the CSE time-course while controlling for mnemonic influences. Existing attention-based accounts of CSEs are either ambiguous in their predictions of CSE time-courses, or predict CSEs to persist or grow over the post-stimulus/response interval in anticipation of an upcoming stimulus. We gauged CSE time-courses by systematically varying inter-stimulus (Experiment 1 and response-to-stimulus (Experiment 2 intervals across a wide temporal range, in a face-word Stroop task. In spite of a an exponential increase in the likelihood of stimulus appearance with increasing interval duration (i.e., an exponential hazard function, results from both experiments showed CSEs to be most pronounced at the shortest intervals, to quickly decay in magnitude with increasing interval length, and to be absent at longer intervals. These data refute the idea that attentional contributions to CSEs remain static over post-stimulus/response intervals and are incompatible with the notion that CSEs reflect expectation-guided preparatory biasing in anticipation of a forthcoming stimulus. The data are compatible, however, with the notion that attentional contributions to CSEs reflect a short-lived, phasic enhancement of attentional set in reaction to processing conflict.

  20. Small RNA transcriptome investigation based on next-generation sequencing technology

    Institute of Scientific and Technical Information of China (English)

    Linglin Zhou; Xueying Li; Qi Liu; Fangqing Zhao; Jinyu Wu

    2011-01-01

    Over the past decade,there has been a growing realization that studying the small RNA transcriptome is essential for understanding the complexity of transcriptional regulation.With an increased throughput and a reduced cost,next-generation sequencing technology has provided an unprecedented opportunity to measure the extent and complexity of small RNA transcriptome.Meanwhile,the large amount of obtained data and varied technology platforms have also posed multiple challenges for effective data analysis and mining.To provide some insight into the small RNA transcriptome investigation,this review describes the major small RNA classes,experimental methods to identify small RNAs,and available bioinformatics tools and databases.

  1. LOESS correction for length variation in gene set-based genomic sequence analysis

    OpenAIRE

    Aboukhalil, Anton; Bulyk, Martha L.

    2012-01-01

    Motivation: Sequence analysis algorithms are often applied to sets of DNA, RNA or protein sequences to identify common or distinguishing features. Controlling for sequence length variation is critical to properly score sequence features and identify true biological signals rather than length-dependent artifacts.

  2. Changes in DNA base sequence induced by gamma-ray mutagenesis of lambda phage and prophage

    International Nuclear Information System (INIS)

    Mutations in the cI (repressor) gene were induced by gamma-ray irradiation of lambda phage and of prophage, and 121 mutations were sequenced. Two-thirds of the mutations in irradiated phage assayed in recA host cells (no induction of the SOS response) were G:C to A:T transitions; it is hypothesized that these may arise during DNA replication from adenine mispairing with a cytosine product deaminated by irradiation. For irradiated phage assayed in host cells in which the SOS response had been induced, 85% of the mutations were base substitutions, and in 40 of the 41 base changes, a preexisting base pair had been replaced by an A:T pair; these might come from damaged bases acting as AP (apurinic or apyrimidinic) sites. The remaining mutations were 1 and 2 base deletions. In irradiated prophage, base change mutations involved the substitution of both A:T and of G:C pairs for the preexisting pairs; the substitution of G:C pairs shows that some base substitution mechanism acts on the cell genome but not on the phage. In the irradiated prophage, frameshifts and a significant number of gross rearrangements were also found

  3. Model for predicting non-linear crack growth considering load sequence effects (LOSEQ)

    International Nuclear Information System (INIS)

    A new analytical model for predicting non-linear crack growth is presented which takes into account the retardation as well as the acceleration effects due to irregular loading. It considers not only the maximum peak of a load sequence to effect crack growth but also all other loads of the history according to a generalised memory criterion. Comparisons between crack growth predicted by using the LOSEQ-programme and experimentally observed data are presented. (orig.)

  4. Effects of sleep loss, time of day, and extended mental work on implicit and explicit learning of sequences

    Science.gov (United States)

    Heuer, H.; Spijkers, W.; Kiesswetter, E.; Schmidtke, V.

    1998-01-01

    Tacit knowledge is part of many professional skills and can be studied experimentally with implicit-learning paradigms. The authors explored the effects of 2 different stressors, loss of sleep and mental fatigue, on implicit learning in a serial-response time (RT) task. In the 1st experiment, 1 night of sleep deprivation was shown to impair implicit but not explicit sequence learning. In the 2nd experiment, no impairment of both types of sequence learning was found after 1.5 hr of mental work. Serial-RT performance, in contrast, suffered from both stressors. These findings suggest that sleep deprivation induces specific risks for automatic, skill-based behavior that are not present in consciously controlled performance.

  5. Cytochrome oxidase-I sequence based studies of commercially available Pangasius hypophthalmus in Italy

    Directory of Open Access Journals (Sweden)

    Federica Bellagamba

    2015-09-01

    Full Text Available Pangasius hypophthalmus is one of the fish consumed in the Italian diet. It is farmed and imported from Mekong delta region of Vietnam. Among several types of Pangasius, Tra (Pangasius hypophthalmus is permitted for sales by the European Union. Since these fish species are often allegedly substituted with other morphologically similar fish due to commercial benefits, authentication of the products in the international markets become often necessary to prevent fraud and safety issues. In addition, this fish is imported as fillets without skin and bone, thus leaving the consumer’s at the risk of buying a substandard nutritional food. In this article we present the molecular approach we developed to identify Pangasius hypophthalmus from other closely related species based on cytochrome oxidase-I (COI mitochondrial barcoding gene and further described the variants in the studied population genetic of this species. Fifty-one samples of Pangasius hypophthalmus fillets labelled as Pangasio were obtained from various markets around Milan and their COI mitochondrial barcoding gene was sequenced and studied in our bioinformatics pipeline. All samples were successfully amplified and Basic Local Alignment Search Tool results of the amplified region confirmed that all sequences analysed belonged to Pangasius hypophthalmus. Based on the variations in their barcoding region single nucleotide polymorphisms were identified and delineative statistics was calculated on the sequences. Although Pangasius hypophthalmus is considered as a monophyly, seven polymorphisms were identified. The neighbour-joining tree and the Median-joining network of haplotypes showed for all the identified haplotypes a unique cluster, with the exception of one sample.

  6. Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies.

    Science.gov (United States)

    Damiati, E; Borsani, G; Giacopuzzi, Edoardo

    2016-05-01

    The Ion Proton platform allows to perform whole exome sequencing (WES) at low cost, providing rapid turnaround time and great flexibility. Products for WES on Ion Proton system include the AmpliSeq Exome kit and the recently introduced HiQ sequencing chemistry. Here, we used gold standard variants from GIAB consortium to assess the performances in variants identification, characterize the erroneous calls and develop a filtering strategy to reduce false positives. The AmpliSeq Exome kit captures a large fraction of bases (>94 %) in human CDS, ClinVar genes and ACMG genes, but with 2,041 (7 %), 449 (13 %) and 11 (19 %) genes not fully represented, respectively. Overall, 515 protein coding genes contain hard-to-sequence regions, including 90 genes from ClinVar. Performance in variants detection was maximum at mean coverage >120×, while at 90× and 70× we measured a loss of variants of 3.2 and 4.5 %, respectively. WES using HiQ chemistry showed ~71/97.5 % sensitivity, ~37/2 % FDR and ~0.66/0.98 F1 score for indels and SNPs, respectively. The proposed low, medium or high-stringency filters reduced the amount of false positives by 10.2, 21.2 and 40.4 % for indels and 21.2, 41.9 and 68.2 % for SNP, respectively. Amplicon-based WES on Ion Proton platform using HiQ chemistry emerged as a competitive approach, with improved accuracy in variants identification. False-positive variants remain an issue for the Ion Torrent technology, but our filtering strategy can be applied to reduce erroneous variants. PMID:27003585

  7. iTriplet, a rule-based nucleic acid sequence motif finder

    Directory of Open Access Journals (Sweden)

    Gunderson Samuel I

    2009-10-01

    Full Text Available Abstract Background With the advent of high throughput sequencing techniques, large amounts of sequencing data are readily available for analysis. Natural biological signals are intrinsically highly variable making their complete identification a computationally challenging problem. Many attempts in using statistical or combinatorial approaches have been made with great success in the past. However, identifying highly degenerate and long (>20 nucleotides motifs still remains an unmet challenge as high degeneracy will diminish statistical significance of biological signals and increasing motif size will cause combinatorial explosion. In this report, we present a novel rule-based method that is focused on finding degenerate and long motifs. Our proposed method, named iTriplet, avoids costly enumeration present in existing combinatorial methods and is amenable to parallel processing. Results We have conducted a comprehensive assessment on the performance and sensitivity-specificity of iTriplet in analyzing artificial and real biological sequences in various genomic regions. The results show that iTriplet is able to solve challenging cases. Furthermore we have confirmed the utility of iTriplet by showing it accurately predicts polyA-site-related motifs using a dual Luciferase reporter assay. Conclusion iTriplet is a novel rule-based combinatorial or enumerative motif finding method that is able to process highly degenerate and long motifs that have resisted analysis by other methods. In addition, iTriplet is distinguished from other methods of the same family by its parallelizability, which allows it to leverage the power of today's readily available high-performance computing systems.

  8. Neuronal substrate and effective connectivity of abnormal movement sequencing in schizophrenia.

    Science.gov (United States)

    Zemankova, Petra; Lungu, Ovidiu; Huttlova, Jitka; Kerkovsky, Milos; Zubor, Jozef; Lipova, Petra; Bares, Martin; Kasparek, Tomas

    2016-06-01

    Movement sequencing difficulties are part of the neurological soft signs (NSS), they have high clinical value because they are not always present in schizophrenia. We investigated the neuronal correlates of movement sequencing in 24 healthy controls and 24 schizophrenia patients, with (SZP SQ+) or without (SZP SQ-) sequencing difficulties. We characterized simultaneous and lagged functional connectivity between brain regions involved in movement sequencing using psychophysiological interaction (PPI) and the Granger causality modeling (GCM), respectively. Left premotor cortex (PMC) and superior parietal lobule (SPL) were specifically activated during sequential movements in all participants. Right PMC and precuneus, ipsilateral to the hand executing the task, activated during sequential movements only in healthy controls and SZP SQ-. SZP SQ+ showed hyperactivation in contralateral PMC, as compared to the other groups. PPI analysis revealed a deficit in inhibitory connections within this fronto-parietal network in SZP SQ+ during sequential task. GCM showed a significant lagged effective connectivity from right PMC to left SPL during task and rest periods in all groups and from right PMC to right precuneus in SZP SQ+ group only. Both SZP groups had a significant lagged connectivity from right to left PMC, during sequential task. Our results indicate that aberrant fronto-parietal network connectivity with cortical inhibition deficit and abnormal reliance on previous network activity are related to movement sequencing in SZP. The overactivation of motor cortex seems to be a good compensating strategy, the hyperactivation of parietal cortex is linked to motor deficit symptoms. PMID:26780603

  9. Application of Sequence-based Methods in Human MicrobialEcology

    Energy Technology Data Exchange (ETDEWEB)

    Weng, Li; Rubin, Edward M.; Bristow, James

    2005-08-29

    Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because DNA based-techniques for defining uncultured microbes allow not only cataloging of microbial diversity, but also insight into microbial functions, investigators are beginning to apply these tools to the microbial communities that abound on and within us, in what has aptly been called the second Human Genome Project. In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

  10. Evaluation of the Terminal Sequencing and Spacing System for Performance Based Navigation Arrivals

    Science.gov (United States)

    Thipphavong, Jane; Jung, Jaewoo; Swenson, Harry N.; Martin, Lynne; Lin, Melody; Nguyen, Jimmy

    2013-01-01

    NASA has developed the Terminal Sequencing and Spacing (TSS) system, a suite of advanced arrival management technologies combining timebased scheduling and controller precision spacing tools. TSS is a ground-based controller automation tool that facilitates sequencing and merging arrivals that have both current standard ATC routes and terminal Performance-Based Navigation (PBN) routes, especially during highly congested demand periods. In collaboration with the FAA and MITRE's Center for Advanced Aviation System Development (CAASD), TSS system performance was evaluated in human-in-the-loop (HITL) simulations with currently active controllers as participants. Traffic scenarios had mixed Area Navigation (RNAV) and Required Navigation Performance (RNP) equipage, where the more advanced RNP-equipped aircraft had preferential treatment with a shorter approach option. Simulation results indicate the TSS system achieved benefits by enabling PBN, while maintaining high throughput rates-10% above baseline demand levels. Flight path predictability improved, where path deviation was reduced by 2 NM on average and variance in the downwind leg length was 75% less. Arrivals flew more fuel-efficient descents for longer, spending an average of 39 seconds less in step-down level altitude segments. Self-reported controller workload was reduced, with statistically significant differences at the p less than 0.01 level. The RNP-equipped arrivals were also able to more frequently capitalize on the benefits of being "Best-Equipped, Best- Served" (BEBS), where less vectoring was needed and nearly all RNP approaches were conducted without interruption.

  11. MuffinInfo: HTML5-Based Statistics Extractor from Next-Generation Sequencing Data.

    Science.gov (United States)

    Alic, Andy S; Blanquer, Ignacio

    2016-09-01

    Usually, the information known a priori about a newly sequenced organism is limited. Even resequencing the same organism can generate unpredictable output. We introduce MuffinInfo, a FastQ/Fasta/SAM information extractor implemented in HTML5 capable of offering insights into next-generation sequencing (NGS) data. Our new tool can run on any software or hardware environment, in command line or graphically, and in browser or standalone. It presents information such as average length, base distribution, quality scores distribution, k-mer histogram, and homopolymers analysis. MuffinInfo improves upon the existing extractors by adding the ability to save and then reload the results obtained after a run as a navigable file (also supporting saving pictures of the charts), by supporting custom statistics implemented by the user, and by offering user-adjustable parameters involved in the processing, all in one software. At the moment, the extractor works with all base space technologies such as Illumina, Roche, Ion Torrent, Pacific Biosciences, and Oxford Nanopore. Owing to HTML5, our software demonstrates the readiness of web technologies for mild intensive tasks encountered in bioinformatics. PMID:27606794

  12. Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment

    Directory of Open Access Journals (Sweden)

    Manzini Giovanni

    2007-07-01

    Full Text Available Abstract Background Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric has gained prominence. It is based on the deep theory of Kolmogorov Complexity and universality is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rather than a formula quantifying the similarity of two strings. Three approximations of USM are available, namely UCD (Universal Compression Dissimilarity, NCD (Normalized Compression Dissimilarity and CD (Compression Dissimilarity. Their applicability and robustness is tested on various data sets yielding a first massive quantitative estimate that the USM methodology and its approximations are of value. Despite the rich theory developed around USM, its experimental assessment has limitations: only a few data compressors have been tested in conjunction with USM and mostly at a qualitative level, no comparison among UCD, NCD and CD is available and no comparison of USM with existing methods, both based on alignments and not, seems to be available. Results We experimentally test the USM methodology by using 25 compressors, all three of its known approximations and six data sets of relevance to Molecular Biology. This offers the first systematic and quantitative experimental assessment of this methodology, that naturally complements the many theoretical and the preliminary experimental results available. Moreover, we compare the USM methodology both with methods based on alignments and not. We may group our experiments into two sets. The first one, performed via ROC

  13. Environment map building and localization for robot navigation based on image sequences

    Institute of Scientific and Technical Information of China (English)

    Ye-hu SHEN; Ji-lin LIU; Xin DU

    2008-01-01

    SLAM is one of the most important components in robot navigation. A SLAM algorithm based on image sequences captured by a single digital camera is proposed in this paper. By this algorithm, SIFT feature points are selected and matched between image pairs sequentially. After three images have been captured, the environment's 3D map and the camera's positions are initialized based on matched feature points and intrinsic parameters of the camera. A robust method is applied to estimate the position and orientation of the camera in the forthcoming images. Finally, a robust adaptive bundle adjustment algorithm is adopted to optimize the environment's 3D map and the camera's positions simultaneously. Results of quantitative and qualitative experiments show that our algorithm can reconstruct the environment and localize the camera accurately and efficiently.

  14. Repetitive sequence based polymerase chain reaction to differentiate close bacteria strains in acidic sites

    Institute of Scientific and Technical Information of China (English)

    XIE Ming; YIN Hua-qun; LIU Yi; LIU Jie; LIU Xue-duan

    2008-01-01

    To study the diversity of bacteria strains newly isolated from several acid mine drainage(AMD) sites in China,repetitive sequence based polymerase chain reaction (rep-PCR),a well established technology for diversity analysis of closely related bacteria strains,was conducted on 30 strains of bacteria Leptospirillum ferriphilium,8 strains of bacteria Acidithiobacillus ferrooxidans,as well as the Acidithiobacillus ferrooxidans type strain ATCC (American Type Culture Collection) 23270.The results showed that,using ERIC and BOX primer sets,rep-PCR produced highly discriminatory banding patterns.Phylogenetic analysis based on ERIC-PCR banding types was made and the results indicated that rep-PCR could be used as a rapid and highly discriminatory screening technique in studying bacterial diversity,especially in differentiating bacteria within one species in AMD.

  15. Channels Reallocation In Cognitive Radio Networks Based On DNA Sequence Alignment

    CERN Document Server

    Singh, Santosh Kumar; Pathak, Vibhakar; 10.5121/ijngn.2010.2203

    2010-01-01

    Nowadays, It has been shown that spectrum scarcity increased due to tremendous growth of new players in wireless base system by the evolution of the radio communication. Resent survey found that there are many areas of the radio spectrum that are occupied by authorized user/primary user (PU), which are not fully utilized. Cognitive radios (CR) prove to next generation wireless communication system that proposed as a way to reuse this under-utilised spectrum in an opportunistic and non-interfering basis. A CR is a self-directed entity in a wireless communications environment that senses its environment, tracks changes, and reacts upon its findings and frequently exchanges information with the networks for secondary user (SU). However, CR facing collision problem with tracks changes i.e. reallocating of other empty channels for SU while PU arrives. In this paper, channels reallocation technique based on DNA sequence alignment algorithm for CR networks has been proposed.

  16. Negative Sequence Droop Method based Hierarchical Control for Low Voltage Ride-Through in Grid-Interactive Microgrids

    DEFF Research Database (Denmark)

    Zhao, Xin; Firoozabadi, Mehdi Savaghebi; Quintero, Juan Carlos Vasquez; Guerrero, Josep M.; Sun, Kai; Wu, Xiaohua; Chen, Guoliang; Sun, Libing

    this paper, a voltage support strategy based on negative sequence droop control, which regulate the positive/negative sequence active and reactive power flow by means of sending proper voltage reference to the inner control loop, is proposed for the grid connected MGs to ride through voltage sags under...... control loop consists of voltage and current inner loops, conventional droop control and virtual impedance loop while the secondary control loop is based on positive/negative sequence droop control which can achieve power injection under voltage sags. Experimental results with asymmetrical voltage sags...

  17. Modeling and optimizing periodically inspected software rejuvenation policy based on geometric sequences

    International Nuclear Information System (INIS)

    Software aging is characterized by an increasing failure rate, progressive performance degradation and even a sudden crash in a long-running software system. Software rejuvenation is an effective method to counteract software aging. A periodically inspected rejuvenation policy for software systems is studied. The consecutive inspection intervals are assumed to be a decreasing geometric sequence, and upon the inspection times of software system and its failure features, software rejuvenation or system recovery is performed. The system availability function and cost rate function are obtained, and the optimal inspection time and rejuvenation interval are both derived to maximize system availability and minimize cost rate. Then, boundary conditions of the optimal rejuvenation policy are deduced. Finally, the numeric experiment result shows the effectiveness of the proposed policy. Further compared with the existing software rejuvenation policy, the new policy has higher system availability. - Highlights: • A periodically inspected rejuvenation policy for software systems is studied. • A decreasing geometric sequence is used to denote the consecutive inspection intervals. • The optimal inspection times and rejuvenation interval are found. • The new policy is capable of reducing average cost and improving system availability

  18. A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

    Directory of Open Access Journals (Sweden)

    Benson Andrew K

    2010-12-01

    Full Text Available Abstract Background We propose a sequence clustering algorithm and compare the partition quality and execution time of the proposed algorithm with those of a popular existing algorithm. The proposed clustering algorithm uses a grammar-based distance metric to determine partitioning for a set of biological sequences. The algorithm performs clustering in which new sequences are compared with cluster-representative sequences to determine membership. If comparison fails to identify a suitable cluster, a new cluster is created. Results The performance of the proposed algorithm is validated via comparison to the popular DNA/RNA sequence clustering approach, CD-HIT-EST, and to the recently developed algorithm, UCLUST, using two different sets of 16S rDNA sequences from 2,255 genera. The proposed algorithm maintains a comparable CPU execution time with that of CD-HIT-EST which is much slower than UCLUST, and has successfully generated clusters with higher statistical accuracy than both CD-HIT-EST and UCLUST. The validation results are especially striking for large datasets. Conclusions We introduce a fast and accurate clustering algorithm that relies on a grammar-based sequence distance. Its statistical clustering quality is validated by clustering large datasets containing 16S rDNA sequences.

  19. Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data

    Directory of Open Access Journals (Sweden)

    Staud Roland

    2009-08-01

    Full Text Available Abstract Single nucleotide polymorphisms (SNPs represent the most widespread type of DNA sequence variation in the human genome and they have recently emerged as valuable genetic markers for revealing the genetic architecture of complex traits in terms of nucleotide combination and sequence. Here, we extend an algorithmic model for the haplotype analysis of SNPs to estimate the effects of genetic imprinting expressed at the DNA sequence level. The model provides a general procedure for identifying the number and types of optimal DNA sequence variants that are expressed differently due to their parental origin. The model is used to analyze a genetic data set collected from a pain genetics project. We find that DNA haplotype GAC from three SNPs, OPRKG36T (with two alleles G and T, OPRKA843G (with alleles A and G, and OPRKC846T (with alleles C and T, at the kappa-opioid receptor, triggers a significant effect on pain sensitivity, but with expression significantly depending on the parent from which it is inherited (p = 0.008. With a tremendous advance in SNP identification and automated screening, the model founded on haplotype discovery and statistical inference may provide a useful tool for genetic analysis of any quantitative trait with complex inheritance.

  20. Use of tritiated prostaglandins in metabolism studies. II: Kinetic isotope effect: an useful tool to investigate catabolizing sequence of prostaglandins

    International Nuclear Information System (INIS)

    It is well established that prostaglandin catabolism involves sequential actions of a 15-hydroxyprostaglandin dehydrogenase, a 15-keto-prostaglandin delta 13-reductase and a 15-ketoprostaglandin reductase. This pathway must be confirmed in never investigated tissues before any enzyme assay is carried out. We have developed a new, simple, rapid and reliable method to investigate catabolizing sequence of prostaglandins based on the tritium kinetic isotope effect which occurs during the oxidation of the 15-hydroxyl group of the prostaglandin into a 15-keto group

  1. Origin and phylogenetic analysis of Tibetan Mastiff based on the mitochondrial DNA sequence

    Institute of Scientific and Technical Information of China (English)

    Qifa Li; Zhuang Xie; Zhenshan Liu; Yinxia Li; Xingbo Zhao; Liyan Dong; Zengxiang Pan; Yuanrong Sun; Ning Li; Yinxue Xu

    2008-01-01

    At present, the Tibetan Mastiff is the oldest and most ferocious dog in the world. However, the origin of the Tibetan Mastiff and its Phylogenetic relationship with other large breed dogs such as Saint Bernard are unclear. In this study, the primers were designed according to the mitochondrial genome sequence of the domestic dog, and the 2,525 bp mitochondrial sequence, containing the whole sequence of Cytochrome b, tRNA-Thr, tRNA-Pro, and control region of the Tibetan Mastiff, was obtained. Using grey wolves and coyotes as outgroups, the Tibetan Mastiff and 12 breeds of domestic dogs were analyzed in phylogenesis. Tibetan Mastiff, domestic dog breeds, and grey wolves were clustered into a group and coyotes were clustered in a group separately. This indicated that the Tibetan Mastiff and the other domestic dogs originated from the grey wolf, and the Tibetan Mastiff belonged to Carnivora, Canidae, Canis, Canis lupus, Canis lupus familiaris on the animal taxonomy. In domestic dogs, the middle and small breed dogs were clustered at first; German Sheepdog, Swedish Elkhound, and Black Russian Terrier were clustered into one group, and the Tibetan Mastiff, Old English Sheepdog, Leonberger, and Saint Bernard were clustered in another group. This confirmed the viewpoint that many of the famous large breed dogs worldwide Such as Saint Bernard possibly had the blood lineage of the Tibetan Mastiff, based on the molecular data. According to the substitution rate, we concluded that the approximate divergence time between Tibetan Mastiff and grey wolf was 58,000 years before the present (YBP), and the approximate divergence time between other domestic dogs and grey wolf was 42,000 YBP, demonstrating that the time of origin of the Tibetan Mastiff was earlier than that of the other domestic dogs.

  2. Event-related potential indices of congruency sequence effects without feature integration or contingency learning confounds.

    Science.gov (United States)

    Larson, Michael J; Clayson, Peter E; Kirwan, C Brock; Weissman, Daniel H

    2016-06-01

    The congruency effect in Stroop-like tasks (i.e., increased response time and reduced accuracy in incongruent relative to congruent trials) is often smaller when the previous trial was incongruent as compared to congruent. This congruency sequence effect (CSE) is thought to reflect cognitive control processes that shift attention to the target and/or modulate the response engendered by the distracter differently after incongruent relative to congruent trials. The neural signatures of CSEs are therefore usually attributed to cognitive control processes that minimize distraction from irrelevant stimuli. However, CSEs in previous functional neuroimaging studies were ubiquitously confounded with feature integration and/or contingency learning processes. We therefore investigated whether a neural CSE can be observed without such confounds in a group of healthy young adults (n = 56). To this end, we combined a prime-probe task that lacks such confounds with high-density ERPs to identify, for the first time, the neural time course of confound-minimized CSEs. Replicating recent behavioral findings, we observed strong CSEs in this task for mean response time and mean accuracy. Critically, conceptually replicating prior ERP results from confounded tasks, we also observed a CSE in both the parietal conflict slow potential (conflict SP) and the frontomedial N450. These findings indicate for the first time that neural CSEs as indexed by ERPs can be observed without the typical confounds. More broadly, the present study provides a confound-minimized protocol that will help future researchers to better isolate the neural bases of control processes that minimize distraction from irrelevant stimuli. PMID:26854028

  3. Principles and procedures of considering item sequence effects in the development of calibrated item pools: Conceptual analysis and empirical illustration

    Directory of Open Access Journals (Sweden)

    Safir Yousfi

    2012-12-01

    Full Text Available Item responses can be context-sensitive. Consequently, composing test forms flexibly from a calibrated item pool requires considering potential context effects. This paper focuses on context effects that are related to the item sequence. It is argued that sequence effects are not necessarily a violation of item response theory but that item response theory offers a powerful tool to analyze them. If sequence effects are substantial, test forms cannot be composed flexibly on the basis of a calibrated item pool, which precludes applications like computerized adaptive testing. In contrast, minor sequence effects do not thwart applications of calibrated item pools. Strategies to minimize the detrimental impact of sequence effects on item parameters are discussed and integrated into a nomenclature that addresses the major features of item calibration designs. An example of an item calibration design demonstrates how this nomenclature can guide the process of developing a calibrated item pool.

  4. Digital Sequences and a Time Reversal-Based Impact Region Imaging and Localization Method

    Directory of Open Access Journals (Sweden)

    Weifeng Qian

    2013-10-01

    Full Text Available To reduce time and cost of damage inspection, on-line impact monitoring of aircraft composite structures is needed. A digital monitor based on an array of piezoelectric transducers (PZTs is developed to record the impact region of impacts on-line. It is small in size, lightweight and has low power consumption, but there are two problems with the impact alarm region localization method of the digital monitor at the current stage. The first one is that the accuracy rate of the impact alarm region localization is low, especially on complex composite structures. The second problem is that the area of impact alarm region is large when a large scale structure is monitored and the number of PZTs is limited which increases the time and cost of damage inspections. To solve the two problems, an impact alarm region imaging and localization method based on digital sequences and time reversal is proposed. In this method, the frequency band of impact response signals is estimated based on the digital sequences first. Then, characteristic signals of impact response signals are constructed by sinusoidal modulation signals. Finally, the phase synthesis time reversal impact imaging method is adopted to obtain the impact region image. Depending on the image, an error ellipse is generated to give out the final impact alarm region. A validation experiment is implemented on a complex composite wing box of a real aircraft. The validation results show that the accuracy rate of impact alarm region localization is approximately 100%. The area of impact alarm region can be reduced and the number of PZTs needed to cover the same impact monitoring region is reduced by more than a half.

  5. Cluster based on sequence comparison of homologous proteins of 95 organism species - Gclust Server | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Gclust Server Cluster based on sequence comparison of homologous proteins of 95 organism species Data detail... Data name Cluster based on sequence comparison of homologous proteins of 95 organism species Description of...e History of This Database Site Policy | Contact Us Cluster based on sequence comparison of homologous proteins of 95 organism species - Gclust Server | LSDB Archive ...

  6. Molecular phylogenetic analysis of Indonesia Solanaceae based on DNA sequences of internal transcribed spacer region

    Science.gov (United States)

    Hidayat, Topik; Priyandoko, Didik; Islami, Dina Karina; Wardiny, Putri Yunitha

    2016-02-01

    Solanaceae is one of largest family in Angiosperm group with highly diverse in morphological character. In Indonesia, this group of plant is very popular due to its usefulness as food, ornamental and medicinal plants. However, investigation on phylogenetic relationship among the member of this family in Indonesia remains less attention. The purpose of this study was to evaluate the phylogenetics relationship of the family especially distributed in Indonesia. DNA sequences of Internal Transcribed Spacer (ITS) region of 19 species of Solanaceae and three species of outgroup, which belongs to family Convolvulaceae, Apocynaceae, and Plantaginaceae, were isolated, amplified, and sequenced. Phylogenetic tree analysis based on parsimony method was conducted with using data derived from the ITS-1, 5.8S, and ITS-2, separately, and the combination of all. Results indicated that the phylogenetic tree derived from the combined data established better pattern of relationship than separate data. Thus, three major groups were revealed. Group 1 consists of tribe Datureae, Cestreae, and Petunieae, whereas group 2 is member of tribe Physaleae. Group 3 belongs to tribe Solaneae. The use of the ITS region as a molecular markers, in general, support the global Solanaceae relationship that has been previously reported.

  7. Prevalence and Sequence-Based Identity of Rumen Fluke in Cattle and Deer in New Caledonia.

    Directory of Open Access Journals (Sweden)

    Laura Cauquil

    Full Text Available An abattoir survey was performed in the French Melanesian archipelago of New Caledonia to determine the prevalence of paramphistomes in cattle and deer and to generate material for molecular typing at species and subspecies level. Prevalence in adult cattle was high at animal level (70% of 387 adult cattle and batch level (81%. Prevalence was lower in calves at both levels (33% of 484 calves, 51% at batch level. Animals from 2 of 7 deer farms were positive for rumen fluke, with animal-level prevalence of 41.4% (29/70 and 47.1% (33/70, respectively. Using ITS-2 sequencing, 3 species of paramphistomes were identified, i.e. Calicophoron calicophorum, Fischoederius elongatus and Orthocoelium streptocoelium. All three species were detected in cattle as well as deer, suggesting the possibility of rumen fluke transmission between the two host species. Based on heterogeneity in ITS-2 sequences, the C. calicophorum population comprises two clades, both of which occur in cattle as well as deer. The results suggest two distinct routes of rumen fluke introduction into this area. This approach has wider applicability for investigations of the origin of rumen fluke infections and for the possibility of parasite transmission at the livestock-wildlife interface.

  8. Sequencing-based approach identified three new susceptibility loci for psoriasis.

    Science.gov (United States)

    Sheng, Yujun; Jin, Xin; Xu, Jinhua; Gao, Jinping; Du, Xiaoqing; Duan, Dawei; Li, Bing; Zhao, Jinhua; Zhan, Wenying; Tang, Huayang; Tang, Xianfa; Li, Yang; Cheng, Hui; Zuo, Xianbo; Mei, Junpu; Zhou, Fusheng; Liang, Bo; Chen, Gang; Shen, Changbing; Cui, Hongzhou; Zhang, Xiaoguang; Zhang, Change; Wang, Wenjun; Zheng, Xiaodong; Fan, Xing; Wang, Zaixing; Xiao, Fengli; Cui, Yong; Li, Yingrui; Wang, Jun; Yang, Sen; Xu, Lei; Sun, Liangdan; Zhang, Xuejun

    2014-01-01

    In a previous large-scale exome sequencing analysis for psoriasis, we discovered seven common and low-frequency missense variants within six genes with genome-wide significance. Here we describe an in-depth analysis of noncoding variants based on sequencing data (10,727 cases and 10,582 controls) with replication in an independent cohort of Han Chinese individuals consisting of 4,480 cases and 6,521 controls to identify additional psoriasis susceptibility loci. We confirmed four known psoriasis susceptibility loci (IL12B, IFIH1, ERAP1 and RNF114; 2.30 × 10(-20)≤P≤2.41 × 10(-7)) and identified three new susceptibility loci: 4q24 (NFKB1) at rs1020760 (P=2.19 × 10(-8)), 12p13.3 (CD27-LAG3) at rs758739 (P=4.08 × 10(-8)) and 17q12 (IKZF3) at rs10852936 (P=1.96 × 10(-8)). Two suggestive loci, 3p21.31 and 17q25, are also identified with P<1.00 × 10(-6). The results of this study increase the number of confirmed psoriasis risk loci and provide novel insight into the pathogenesis of psoriasis. PMID:25006012

  9. Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences

    Science.gov (United States)

    Ogilvie, Lesley A.; Bowler, Lucas D.; Caplin, Jonathan; Dedi, Cinzia; Diston, David; Cheek, Elizabeth; Taylor, Huw; Ebdon, James E.; Jones, Brian V.

    2013-01-01

    Bacterial viruses (bacteriophages) have a key role in shaping the development and functional outputs of host microbiomes. Although metagenomic approaches have greatly expanded our understanding of the prokaryotic virosphere, additional tools are required for the phage-oriented dissection of metagenomic data sets, and host-range affiliation of recovered sequences. Here we demonstrate the application of a genome signature-based approach to interrogate conventional whole-community metagenomes and access subliminal, phylogenetically targeted, phage sequences present within. We describe a portion of the biological dark matter extant in the human gut virome, and bring to light a population of potentially gut-specific Bacteroidales-like phage, poorly represented in existing virus like particle-derived viral metagenomes. These predominantly temperate phage were shown to encode functions of direct relevance to human health in the form of antibiotic resistance genes, and provided evidence for the existence of putative ‘viral-enterotypes’ among this fraction of the human gut virome. PMID:24036533

  10. Internal Transcribed Spacer 1 (ITS1 based sequence typing reveals phylogenetically distinct Ascaris population

    Directory of Open Access Journals (Sweden)

    Koushik Das

    2015-01-01

    Full Text Available Taxonomic differentiation among morphologically identical Ascaris species is a debatable scientific issue in the context of Ascariasis epidemiology. To explain the disease epidemiology and also the taxonomic position of different Ascaris species, genome information of infecting strains from endemic areas throughout the world is certainly crucial. Ascaris population from human has been genetically characterized based on the widely used genetic marker, internal transcribed spacer1 (ITS1. Along with previously reported and prevalent genotype G1, 8 new sequence variants of ITS1 have been identified. Genotype G1 was significantly present among female patients aged between 10 to 15 years. Intragenic linkage disequilibrium (LD analysis at target locus within our study population has identified an incomplete LD value with potential recombination events. A separate cluster of Indian isolates with high bootstrap value indicate their distinct phylogenetic position in comparison to the global Ascaris population. Genetic shuffling through recombination could be a possible reason for high population diversity and frequent emergence of new sequence variants, identified in present and other previous studies. This study explores the genetic organization of Indian Ascaris population for the first time which certainly includes some fundamental information on the molecular epidemiology of Ascariasis.

  11. Internal Transcribed Spacer 1 (ITS1) based sequence typing reveals phylogenetically distinct Ascaris population.

    Science.gov (United States)

    Das, Koushik; Chowdhury, Punam; Ganguly, Sandipan

    2015-01-01

    Taxonomic differentiation among morphologically identical Ascaris species is a debatable scientific issue in the context of Ascariasis epidemiology. To explain the disease epidemiology and also the taxonomic position of different Ascaris species, genome information of infecting strains from endemic areas throughout the world is certainly crucial. Ascaris population from human has been genetically characterized based on the widely used genetic marker, internal transcribed spacer1 (ITS1). Along with previously reported and prevalent genotype G1, 8 new sequence variants of ITS1 have been identified. Genotype G1 was significantly present among female patients aged between 10 to 15 years. Intragenic linkage disequilibrium (LD) analysis at target locus within our study population has identified an incomplete LD value with potential recombination events. A separate cluster of Indian isolates with high bootstrap value indicate their distinct phylogenetic position in comparison to the global Ascaris population. Genetic shuffling through recombination could be a possible reason for high population diversity and frequent emergence of new sequence variants, identified in present and other previous studies. This study explores the genetic organization of Indian Ascaris population for the first time which certainly includes some fundamental information on the molecular epidemiology of Ascariasis. PMID:26504510

  12. Safety assessment of Bifidobacterium longum J DM301 based on complete genome sequences

    Institute of Scientific and Technical Information of China (English)

    Yan-Xia Wei; Zhuo-Yang Zhang; Chang Liu; Xiao-Kui Guo; Pradeep K Malakar

    2012-01-01

    AIM: To assess the safety of Bifidobacterium longum (B.longum) JDM301 based on complete genome sequences. METHODS: The complete genome sequences of JDM301 were determined using the GS 20 system. Putative virulence factors, putative antibiotic resistance genes and genes encoding enzymes responsible for harmful metabolites were identified by blast with virulence factors database, antibiotic resistance genes database and genes associated with harmful metabolites in previous reports. Minimum inhibitory concentration of 16 common antimicrobial agents was evaluated by E-test. RESULTS: JDM301 was shown to contain 36 genes associated with antibiotic resistance, 5 enzymes related to harmful metabolites and 162 nonspecific virulence factors mainly associated with transcriptional regulation, adhesion, sugar and amino acid transport. B. longum JDM301 was intrinsically resistant tocipro ciprofloxacin,amikacin, gentamicin and streptomycin and susceptible to vancomycin, amoxicillin, cephalothin, chloramphenicol, erythromycin, ampicillin, cefotaxime, rifampicin, imipenemandtrimethoprim and trimethoprim-sulphamethoxazol. JDM301.JDM301 was moderately resistant to bacitracin, while an earlier study showed that bifidobacteria were susceptible to this antibiotic. A tetracycline resistance gene with the risk of transfer was found in JDM301, which needs to be experimentally validated. CONCLUSION: The safety assessment of JDM301 using information derived from complete bacterial genome will contribute to a wider and deeper insight into the safety of probiotic bacteria.

  13. Molecular phylogeny and evolution of Scomber (Teleostei: Scombridae) based on mitochondrial and nuclear DNA sequences

    Institute of Scientific and Technical Information of China (English)

    CHENG Jiao; GAO Tianxiang; MIAO Zhenqing; YANAGIMOTO Takashi

    2011-01-01

    A molecular phylogenetic analysis of the genus Scomber was conducted based on mitochondrial (COI, Cyt b and control region) and nuclear (5S rDNA) DNA sequence data in multigene perspective. A variety of phylogenetic analytic methods were used to clarify the current taxonomic classification and to assess phylogenetic relationships and the evolutionary history of this genus. The present study produced a well-resolved phylogeny that strongly supported the monophyly of Scomber. We confirmed that S. japonicus and S. colias were genetically distinct. Although morphologically and ecologically similar to S. colias, the molecular data showed that S. japonicus has a greater molecular affinity with S. australasicus, which conflicts with the traditional taxonomy. This phyiogenetic pattern was corroborated by the mtDNA data, but incompletely by the nuclear DNA data. Phylogenetic concordance between the mitochondrial and nuclear DNA regions for the basal nodes supports an Atlantic origin for Scomber. The present-day geographic ranges of the species were compared with the resultant molecular phylogeny derived from partition Bayesian analyses of the combined data sets to evaluate possible dispersal routes of the genus. The present-day geographic distribution of Scomber species might be best ascribed to multiple dispersal events. In addition, our results suggest that phylogenies derived from multiple genes and long sequences exhibited improved phylogenetic resolution, from which we conclude that the phylogenetic reconstruction is a reliable representation of the evolutionary history of Scomber.

  14. Trellis-Based Iterative Adaptive Blind Sequence Estimation for Uncoded/Coded Systems with Differential Precoding

    Directory of Open Access Journals (Sweden)

    Chen Xiao-Ming

    2005-01-01

    Full Text Available We propose iterative, adaptive trellis-based blind sequence estimators, which can be interpreted as reduced-complexity receivers derived from the joint ML data/channel estimation problem. The number of states in the trellis is considered as a design parameter, providing a trade-off between performance and complexity. For symmetrical signal constellations, differential encoding or generalizations thereof are necessary to combat the phase ambiguity. At the receiver, the structure of the super-trellis (representing differential encoding and intersymbol interference is explicitly exploited rather than doing differential decoding just for resolving the problem of phase ambiguity. In uncoded systems, it is shown that the data sequence can only be determined up to an unknown shift index. This shift ambiguity can be resolved by taking an outer channel encoder into account. The average magnitude of the soft outputs from the corresponding channel decoder is exploited to identify the shift index. For frequency-hopping systems over fading channels, a double serially concatenated scheme is proposed, where the inner code is applied to combat the shift ambiguity and the outer code provides time diversity in conjunction with an interburst interleaver.

  15. Systematic positions of Lamiophiomis and Paraphlomis (Lamiaceae) based on nuclear and chloroplast sequences

    Institute of Scientific and Technical Information of China (English)

    Yue-Zhi PAN; Li-Qin FANG; Gang HAO; Jie CAI; Xun GONG

    2009-01-01

    Genera Lamiophlomis and Paraphlomis were originally separated from genus Phlomis s.l. on the basis of particular morphological characteristics. However, their relationship was highly contentious, as evidenced by the literature. In the present paper, the systematic positions of Lamiophlomis, Paraphlomis, and their related genera were assessed based on nuclear internal transcribed spacer (ITS) and chloroplast rpl16 and trnL-F sequence data using maximum parsimony (MP) and Bayesian methods. In total, 24 species representing six genera of the ingroup and outgroup were sampled. Analyses of both separate and combined sequence data were conducted to resolve the systematic relationships of these genera. The results reveal that Lamiophlomis is nested within Phlomis sect. Phlomoides and its genetic status is not supported. With the inclusion of Lamiophlomis rotata in sect. Phlomoides, sections Phlomis and Phlomoides of Phlomis were resolved as monophyletic. Paraphlomis was supported as an inde-pendent genus. However, the resolution of its monophyly conflicted between MP and Bayesian analyses, suggesting the need for expended sampling and further evidence.

  16. The Utility of Specific Markers Based on ITS2 Sequences for Molecular Identification and Detection of Trichogramma spp.

    Institute of Scientific and Technical Information of China (English)

    LI Zheng-xi; SHEN Zuo-rui

    2002-01-01

    The technology based on specific PCR amplification using internal transcribed spacer 2 of nuclear ribosomal DNA for molecular identification and detection of Trichogramma species was studied. Firstly the ITS2s of six Trichogramma species were cloned and sequenced, and the interspecific sequence variation was analyzed. Secondly the ITS2 regions of six geographical populations of T. dendrolimi were cloned and sequenced, and the intraspecific sequence identity was analyzed. The results show that the interspecific variation and intraspecific similarity of ITS2 sequences are very suitable for designation of specific primers at specieslevel. Screening of specific primers for T. dendrolimi leads to final sensitive and stable diagnostic primers. This system lets non-specialists can not only identify adults (males and females), but also identify eggs in parasitized hosts rapidly and accurately, which is impossible by conventional methods. Further development of this protocol can create a complete set of specific primers for different species of the whole genus Trichogramma.

  17. A Novel Approach to Multiple Sequence Alignment Using Multiobjective Evolutionary Algorithm Based on Decomposition.

    Science.gov (United States)

    Zhu, Huazheng; He, Zhongshi; Jia, Yuanyuan

    2016-03-01

    Multiple sequence alignment (MSA) is a fundamental and key step for implementing other tasks in bioinformatics, such as phylogenetic analyses, identification of conserved motifs and domains, structure prediction, etc. Despite the fact that there are many methods to implement MSA, biologically perfect alignment approaches are not found hitherto. This paper proposes a novel idea to perform MSA, where MSA is treated as a multiobjective optimization problem. A famous multiobjective evolutionary algorithm framework based on decomposition is applied for solving MSA, named MOMSA. In the MOMSA algorithm, we develop a new population initialization method and a novel mutation operator. We compare the performance of MOMSA with several alignment methods based on evolutionary algorithms, including VDGA, GAPAM, and IMSA, and also with state-of-the-art progressive alignment approaches, such as MSAprobs, Probalign, MAFFT, Procons, Clustal omega, T-Coffee, Kalign2, MUSCLE, FSA, Dialign, PRANK, and CLUSTALW. These alignment algorithms are tested on benchmark datasets BAliBASE 2.0 and BAliBASE 3.0. Experimental results show that MOMSA can obtain the significantly better alignments than VDGA, GAPAM on the most of test cases by statistical analyses, produce better alignments than IMSA in terms of TC scores, and also indicate that MOMSA is comparable with the leading progressive alignment approaches in terms of quality of alignments. PMID:25700475

  18. An Efficient Genotyping Method in Chicken Based on Genome Reducing and Sequencing

    OpenAIRE

    Liao, Rongrong; Zhen WANG; Chen, Qiang; Tu, Yingying; Chen, Zhenliang; Wang, Qishan; Yang, Changsuo; Zhang, Xiangzhe; Pan, Yuchun

    2015-01-01

    Single nucleotide polymorphisms (SNPs) are essential for identifying the genetic mechanisms of complex traits. In the present study, we applied genotyping by genome reducing and sequencing (GGRS) method to construct a 252-plex sequencing library for SNP discovery and genotyping in chicken. The library was successfully sequenced on an Illumina HiSeq 2500 sequencer with a paired-end pattern; approximately 400 million raw reads were generated, and an average of approximately 1.4 million good rea...

  19. Base-Calling Algorithm with Vocabulary (BCV) Method for Analyzing Population Sequencing Chromatograms

    OpenAIRE

    Fantin, Yuri S.; Neverov, Alexey D; Favorov, Alexander V.; Alvarez-Figueroa, Maria V.; Braslavskaya, Svetlana I.; Gordukova, Maria A.; Karandashova, Inga V.; Kuleshov, Konstantin V.; Myznikova, Anna I; Polishchuk, Maya S.; Reshetov, Denis A.; Voiciehovskaya, Yana A.; Mironov, Andrei A.; Chulanov, Vladimir P.

    2013-01-01

    Sanger sequencing is a common method of reading DNA sequences. It is less expensive than high-throughput methods, and it is appropriate for numerous applications including molecular diagnostics. However, sequencing mixtures of similar DNA of pathogens with this method is challenging. This is important because most clinical samples contain such mixtures, rather than pure single strains. The traditional solution is to sequence selected clones of PCR products, a complicated, time-consuming, and ...

  20. EvoTol: a protein-sequence based evolutionary intolerance framework for disease-gene prioritization

    OpenAIRE

    Rackham, Owen J. L.; Shihab, Hashem A; Johnson, Michael R.; Petretto, Enrico

    2014-01-01

    Methods to interpret personal genome sequences are increasingly required. Here, we report a novel framework (EvoTol) to identify disease-causing genes using patient sequence data from within protein coding-regions. EvoTol quantifies a gene's intolerance to mutation using evolutionary conservation of protein sequences and can incorporate tissue-specific gene expression data. We apply this framework to the analysis of whole-exome sequence data in epilepsy and congenital heart disease, and demon...

  1. Speech serial control in healthy speakers and speakers with hypokinetic or ataxic dysarthria: Effects of sequence length and practice

    Directory of Open Access Journals (Sweden)

    Kevin J Reilly

    2013-10-01

    Full Text Available The current study investigated the processes responsible for selection of sounds and syllables during production of speech sequences in 10 adults with hypokinetic dysarthria from Parkinson’s disease, 5 adults with ataxic dysarthria, and 14 healthy control speakers. Speech production data from a choice reaction time task were analyzed to evaluate the effects of sequence length and practice on speech sound sequencing. Speakers produced sequences that were between one and five syllables in length over five experimental runs of 60 trials each. In contrast to the healthy speakers, speakers with hypokinetic dysarthria demonstrated exaggerated sequence length effects for both inter-syllable intervals (ISIs and speech error rates. Conversely, speakers with ataxic dysarthria failed to demonstrate a sequence length effect on ISIs and were also the only group that did not exhibit practice-related changes in ISIs and speech error rates over the five experimental runs. The exaggerated sequence length effects in the hypokinetic speakers with Parkinson’s disease are consistent with an impairment of action selection during speech sequence production. The absent length effects observed in the speakers with ataxic dysarthria is consistent with previous findings that indicate a limited capacity to buffer speech sequences in advance of their execution. In addition, the lack of practice effects in these speakers suggests that learning-related improvements in the production rate and accuracy of speech sequences involves processing by structures of the cerebellum. Together, the current findings inform models of serial control for speech in healthy speakers and support the notion that sequencing deficits contribute to speech symptoms in speakers with hypokinetic or ataxic dysarthria. In addition, these findings indicate that speech sequencing is differentially impaired in hypokinetic and ataxic dysarthria.

  2. Effective Normalization for Copy Number Variation Detection from Whole Genome Sequencing

    OpenAIRE

    Janevski Angel; Varadan Vinay; Kamalakaran Sitharthan; Banerjee Nilanjana; Dimitrova Nevenka

    2012-01-01

    Abstract Background Whole genome sequencing enables a high resolution view of the human genome and provides unique insights into genome structure at an unprecedented scale. There have been a number of tools to infer copy number variation in the genome. These tools, while validated, also include a number of parameters that are configurable to genome data being analyzed. These algorithms allow for normalization to account for individual and population-specific effects on individual genome CNV e...

  3. Effects of Cooperative Learning on Instructing Magnetism: Analysis of an Experimental Teaching Sequence

    OpenAIRE

    Zafer Tanel; Mustafa Erol

    2008-01-01

    This paper describes methods and the results of a work designed to analyze effectiveness of an experimental teachingsequence on the topic of magnetism. Cooperative learning techniques were employed to experimental group andconventional teaching method was used for control group throughout the teaching sequence. Sampling of the studyconsists of 19-20 years old 100 students at a state university in zmir, Turkey. Levels of pre-knowledge acquired bythe students were evaluated by means of a self-d...

  4. Effect of multiple debonding sequences on shear bond strength of new stainless steel brackets

    OpenAIRE

    Eslamian, Ladan; Borzabadi-Farahani, Ali; Tavakol, Pegah; Tavakol, Ali; Amini, Nazila; Lynch, Edward

    2015-01-01

    Objectives: This in-vitro study aimed at evaluating the effect of three debonding sequences on the shear bond strength (SBS) of new stainless steel (SS) brackets. Materials and Methods: Stainless steel twin brackets (0.022-inch, American Orthodontics, Sheboygan, WI, USA) were bonded with light cure adhesive (Transbond XT, 3M Unitek, St. Paul, MN, USA) to 80 newly extracted human premolars after acid etching with 37% phosphoric acid (30 s). Brackets were debonded with a universal testing machi...

  5. Nitrogen removal in a Sequencing Batch Biofilm Reactor : effect of carbon availability and intermittent aeration

    OpenAIRE

    Vieira, Maria Madalena Costa; Brito, A. G.; R. Nogueira

    2009-01-01

    This study aimed to investigate the effects of carbon availability and intermittent aeration on nitrogen removal in a Sequencing Batch Biofilm Reactor (SBBR). The percentage of nitrogen removal in the SBBRs operating with dump fill and slow fill with optimum intermittent aeration was quite similar, 75.7% and 69.2%, respectively, indicating that intermittent aeration allowed a considerable energy saving without compromising significantly nitrogen removal. Accumulation of stor...

  6. Sequence Effect in Parkinson’s Disease Is Related to Motor Energetic Cost

    OpenAIRE

    Tinaz, Sule; Pillai, Ajay S.; Hallett, Mark

    2016-01-01

    Bradykinesia is the most disabling motor symptom of Parkinson’s disease (PD). The sequence effect (SE), a feature of bradykinesia, refers to the rapid decrement in amplitude and speed of repetitive movements (e.g., gait, handwriting) and is a major cause of morbidity in PD. Previous research has revealed mixed results regarding the role of dopaminergic treatment in the SE. However, external cueing has been shown to improve it. In this study, we aimed to characterize the SE systematically and ...

  7. Effect of internal recirculation velocity in an anaerobic sequencing batch reactor (ASBR)

    OpenAIRE

    G. Z. Maurina; L. M. Rosa; L. L. Beal; C. Baldasso; J. R. Gimenez; Torres, A.P. (Asvin Pérez); M.P. Sousa

    2014-01-01

    This paper discusses the effect of different internal recirculation velocities on the mixture and shear stress on the flocs in an anaerobic sequencing batch reactor (ASBR). Thus, simulations are performed using a computational fluid dynamics (CFD) tool to evaluate this dependency. The analysis of velocities and turbulent kinetic energy indicates that the highest flow evaluated (0.003 m³/s) results in better mixing within the reactor. However, care must be taken with the recycling pipe size, i...

  8. Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads

    OpenAIRE

    Wu Yufeng; Hernández Yözen; Dinakar Sanjiv; Kennedy Justin; Duitama Jorge; Măndoiu Ion I

    2011-01-01

    Abstract Background Recent technology advances have enabled sequencing of individual genomes, promising to revolutionize biomedical research. However, deep sequencing remains more expensive than microarrays for performing whole-genome SNP genotyping. Results In this paper we introduce a new multi-locus statistical model and computationally efficient genotype calling algorithms that integrate shotgun sequencing data with linkage disequilibrium (LD) information extracted from reference populati...

  9. PCR-based study of the presence of Y-chromosome sequences in patients with Ullrich-Turner syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Coto, E.; Menendez, M.J.; Lopez-Larrea, C. [Universidad Complutense, Madrid (Spain)] [and others

    1995-07-03

    The presence of Y chromosome sequences in Ullrich-Turner syndrome (UTS) patients has been suggested in previous work. Karyotype analysis estimated at about 60% of patients with a 45, X constitution and molecular analysis (Southern blot analysis with several Y chromosome probes and PCR of specific sequences) identified the presence of Y chromosome material in about 40% of 45, X patients. We have developed a very sensitive, PCR-based method to detect Y specific sequences in DNA from UTS patients. This protocol permits the detection of a single cell carrying a Y sequence among 10{sup 5} Y-negative cells. We studied 18 UTS patients with 4 Y-specific sequences. In 11 patients we detected a positive amplification for at least one Y sequence. The existence of a simple and sensitive method for the detection of Y sequences has important implications for UTS patients, in view of the risk for some of the females carrying Y chromosome material of developing gonadoblastoma and virilization. Additionally, some of the UTS-associated phenotypes, such as renal anomalies, could be correlated with the presence of Y chromosome-specific sequences. 27 refs., 2 figs., 1 tab.

  10. Molecular typing of Acinetobacter baumannii by automated repetitive-sequence-based PCR

    Directory of Open Access Journals (Sweden)

    Giuseppe Russello

    2011-03-01

    Full Text Available Acinetobacter baumannii has been increasingly reported as a significant causative organism of various nosocomial infections. Here we describe three different outbreaks of multidrug resistant A. baumannii started in the Intensitive Care Unit and then involving other wards of San Carlo Borromeo hospital in Milan, Italy. In order to characterize the clinical strains isolates, molecular typing using semi-automated repetitive-sequence-based PCR (rep-PCR was performed.Among the sixty-one strains analyzed, three main cluster (C1, C2, C3 were detected: C1 included six indistinguishable strains, C2 five and C3 thirty. No correlation was observed between chemosensitivity and ribotyping pattern and an high rate of carbapenems resistance was founded.

  11. Xylariaceae diversity in Thailand and Philippines, based on rDNA sequencing

    Directory of Open Access Journals (Sweden)

    Natarajan Velmurugan

    2013-07-01

    Full Text Available Twenty three different Xylariaceae Tul. & C. Tul were isolated from samples collected from forest zones of Thailand and Philippines. The fungal samples were characterized based on morphological characteristics and nuclear ITS1-5.8S rDNA-ITS2 region sequences. Ten species of Xylaria, two species of Hypoxylon, Biscogniauxia, Rosellinia and one species of Annulohypoxylon and Entonaema were found. Entonaema the distinctive genus of Xylariaceae, isolated in the study from Thailand samples showed a close relationship withXylaria in phylogenetic tree. Xylariaceous species identified at molecular level showed significant similarity of the morphological characters, such as stromal structure, ascal apex and the germ slit of ascospores. In addition, three species of Arthrinium, two species of Pestalotiopsis were also isolated and characterized in the study. A phylogenetic affinity of Pestalotiopsis with Xylariaceae was found.

  12. Geographic Distribution of Leishmania Species in Ecuador Based on the Cytochrome B Gene Sequence Analysis

    Science.gov (United States)

    Kato, Hirotomo; Gomez, Eduardo A.; Martini-Robles, Luiggi; Muzzio, Jenny; Velez, Lenin; Calvopiña, Manuel; Romero-Alvarez, Daniel; Mimori, Tatsuyuki; Uezato, Hiroshi; Hashiguchi, Yoshihisa

    2016-01-01

    A countrywide epidemiological study was performed to elucidate the current geographic distribution of causative species of cutaneous leishmaniasis (CL) in Ecuador by using FTA card-spotted samples and smear slides as DNA sources. Putative Leishmania in 165 samples collected from patients with CL in 16 provinces of Ecuador were examined at the species level based on the cytochrome b gene sequence analysis. Of these, 125 samples were successfully identified as Leishmania (Viannia) guyanensis, L. (V.) braziliensis, L. (V.) naiffi, L. (V.) lainsoni, and L. (Leishmania) mexicana. Two dominant species, L. (V.) guyanensis and L. (V.) braziliensis, were widely distributed in Pacific coast subtropical and Amazonian tropical areas, respectively. Recently reported L. (V.) naiffi and L. (V.) lainsoni were identified in Amazonian areas, and L. (L.) mexicana was identified in an Andean highland area. Importantly, the present study demonstrated that cases of L. (V.) braziliensis infection are increasing in Pacific coast areas. PMID:27410039

  13. Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort

    Science.gov (United States)

    Singh, Jaya; Mishra, Avshesh; Pandian, Arunachalam Jayamuruga; Mallipatna, Ashwin C.; Khetan, Vikas; Sripriya, S.; Kapoor, Suman; Agarwal, Smita; Sankaran, Satish; Katragadda, Shanmukh; Veeramachaneni, Vamsi; Hariharan, Ramesh; Subramanian, Kalyanasundaram

    2016-01-01

    Purpose Retinoblastoma (Rb) is the most common primary intraocular cancer of childhood and one of the major causes of blindness in children. India has the highest number of patients with Rb in the world. Mutations in the RB1 gene are the primary cause of Rb, and heterogeneous mutations are distributed throughout the entire length of the gene. Therefore, genetic testing requires screening of the entire gene, which by conventional sequencing is time consuming and expensive. Methods In this study, we screened the RB1 gene in the DNA isolated from blood or saliva samples of 50 unrelated patients with Rb using the TruSight Cancer panel. Next-generation sequencing (NGS) was done on the Illumina MiSeq platform. Genetic variations were identified using the Strand NGS software and interpreted using the StrandOmics platform. Results We were able to detect germline pathogenic mutations in 66% (33/50) of the cases, 12 of which were novel. We were able to detect all types of mutations, including missense, nonsense, splice site, indel, and structural variants. When we considered bilateral Rb cases only, the mutation detection rate increased to 100% (22/22). In unilateral Rb cases, the mutation detection rate was 30% (6/20). Conclusions Our study suggests that NGS-based approaches increase the sensitivity of mutation detection in the RB1 gene, making it fast and cost-effective compared to the conventional tests performed in a reflex-testing mode.

  14. The historical biogeography of Pteroglossus aracaris (Aves, Piciformes, Ramphastidae based on Bayesian analysis of mitochondrial DNA sequences

    Directory of Open Access Journals (Sweden)

    Sérgio L. Pereira

    2008-01-01

    Full Text Available Most Neotropical birds, including Pteroglossus aracaris, do not have an adequate fossil record to be used as time constraints in molecular dating. Hence, the evolutionary timeframe of the avian biota can only be inferred using alternative time constraints. We applied a Bayesian relaxed clock approach to propose an alternative interpretation for the historical biogeography of Pteroglossus based on mitochondrial DNA sequences, using different combinations of outgroups and time constraints obtained from outgroup fossils, vicariant barriers and molecular time estimates. The results indicated that outgroup choice has little effect on the Bayesian posterior distribution of divergence times within Pteroglossus , that geological and molecular time constraints seem equally suitable to estimate the Bayesian posterior distribution of divergence times for Pteroglossus , and that the fossil record alone overestimates divergence times within the fossil-lacking ingroup. The Bayesian estimates of divergence times suggest that the radiation of Pteroglossus occurred from the Late Miocene to the Pliocene (three times older than estimated by the “standard” mitochondrial rate of 2% sequence divergence per million years, likely triggered by Andean uplift, multiple episodes of marine transgressions in South America, and formation of present-day river basins. The time estimates are in agreement with other Neotropical taxa with similar geographic distributions.

  15. Generating markers based on biotic stress of protein system in and tandem repeats sequence for Aquilaria sp

    International Nuclear Information System (INIS)

    Aquilaria sp. belongs to the Thymelaeaceae family and is well distributed in Asia region. The species has multipurpose use from root to shoot and is an economically important crop, which generates wide interest in understanding genetic diversity of the species. Knowledge on DNA-based markers has become a prerequisite for more effective application of molecular marker techniques in breeding and mapping programs. In this work, both targeted genes and tandem repeat sequences were used for DNA fingerprinting in Aquilaria sp. A total of 100 ISSR (inter simple sequence repeat) primers and 50 combination pairs of specific primers derived from conserved region of a specific protein known as system in were optimized. 38 ISSR primers were found affirmative for polymorphism evaluation study and were generated from both specific and degenerate ISSR primers. And one utmost combination of system in primers showed significant results in distinguishing the Aquilaria sp. In conclusion, polymorphism derived from ISSR profiling and targeted stress genes of protein system in proved as a powerful approach for identification and molecular classification of Aquilaria sp. which will be useful for diversification in identifying any mutant lines derived from nature. (author)

  16. Interaction among apoptosis-associated sequence variants and joint effects on aggressive prostate cancer

    Directory of Open Access Journals (Sweden)

    Lavender Nicole A

    2012-04-01

    Full Text Available Abstract Background Molecular and epidemiological evidence demonstrate that altered gene expression and single nucleotide polymorphisms in the apoptotic pathway are linked to many cancers. Yet, few studies emphasize the interaction of variant apoptotic genes and their joint modifying effects on prostate cancer (PCA outcomes. An exhaustive assessment of all the possible two-, three- and four-way gene-gene interactions is computationally burdensome. This statistical conundrum stems from the prohibitive amount of data needed to account for multiple hypothesis testing. Methods To address this issue, we systematically prioritized and evaluated individual effects and complex interactions among 172 apoptotic SNPs in relation to PCA risk and aggressive disease (i.e., Gleason score ≥ 7 and tumor stages III/IV. Single and joint modifying effects on PCA outcomes among European-American men were analyzed using statistical epistasis networks coupled with multi-factor dimensionality reduction (SEN-guided MDR. The case-control study design included 1,175 incident PCA cases and 1,111 controls from the prostate, lung, colo-rectal, and ovarian (PLCO cancer screening trial. Moreover, a subset analysis of PCA cases consisted of 688 aggressive and 488 non-aggressive PCA cases. SNP profiles were obtained using the NCI Cancer Genetic Markers of Susceptibility (CGEMS data portal. Main effects were assessed using logistic regression (LR models. Prior to modeling interactions, SEN was used to pre-process our genetic data. SEN used network science to reduce our analysis from > 36 million to Results Following LR modeling, eleven and thirteen sequence variants were associated with PCA risk and aggressive disease, respectively. However, none of these markers remained significant after we adjusted for multiple comparisons. Nevertheless, we detected a modest synergistic interaction between AKT3 rs2125230-PRKCQ rs571715 and disease aggressiveness using SEN-guided MDR (p = 0

  17. The effect of music background on the emotional appraisal of film sequences

    Directory of Open Access Journals (Sweden)

    Pavlović Ivanka

    2011-01-01

    Full Text Available In this study the effects of musical background on the emotional appraisal of film sequences was investigated. Four pairs of polar emotions defined in Plutchik’s model were used as basic emotional qualities: joy-sadness, anticipation-surprise, fear-anger, and trust disgust. In the preliminary study eight film sequences and eight music themes were selected as the best representatives of all eight Plutchik’s emotions. In the main experiment the participant judged the emotional qualities of film-music combinations on eight seven-point scales. Half of the combinations were congruent (e.g. joyful film - joyful music, and half were incongruent (e.g. joyful film - sad music. Results have shown that visual information (film had greater effects on the emotion appraisal than auditory information (music. The modulation effects of music background depend on emotional qualities. In some incongruent combinations (joysadness the modulations in the expected directions were obtained (e.g. joyful music reduces the sadness of a sad film, in some cases (anger-fear no modulation effects were obtained, and in some cases (trust-disgust, anticipation-surprise the modulation effects were in an unexpected direction (e.g. trustful music increased the appraisal of disgust of a disgusting film. These results suggest that the appraisals of conjoint effects of emotions depend on the medium (film masks the music and emotional quality (three types of modulation effects.

  18. Field-based assessment of landslide hazards resulting from the 2015 Gorkha, Nepal earthquake sequence

    Science.gov (United States)

    Collins, B. D.; Jibson, R.

    2015-12-01

    The M7.8 2015 Gorkha, Nepal earthquake sequence caused thousands of fatalities, destroyed entire villages, and displaced millions of residents. The earthquake sequence also triggered thousands of landslides in the steep Himalayan topography of Nepal and China; these landslides were responsible for hundreds of fatalities and blocked vital roads, trails, and rivers. With the support of USAID's Office of Foreign Disaster Assistance, the U.S. Geological Survey responded to this crisis by providing landslide-hazard expertise to Nepalese agencies and affected villages. Assessments of landslide hazards following earthquakes are essential to identify vulnerable populations and infrastructure, and inform government agencies working on rebuilding and mitigation efforts. However, assessing landslide hazards over an entire earthquake-affected region (in Nepal, estimated to be ~30,000 km2), and in exceedingly steep, inaccessible topography presents a number of logistical challenges. We focused the scope of our assessment by conducting helicopter- and ground-based landslide assessments in 12 priority areas in central Nepal identified a priori from satellite photo interpretation performed in conjunction with an international consortium of remote sensing experts. Our reconnaissance covered 3,200 km of helicopter flight path, extending over an approximate area of 8,000 km2. During our field work, we made 17 site-specific assessments and provided landslide hazard information to both villages and in-country agencies. Upon returning from the field, we compiled our observations and further identified and assessed 74 river-blocking landslide dams, 12% of which formed impoundments larger than 1,000 m2 in surface area. These assessments, along with more than 11 hours of helicopter-based video, and an overview of hazards expected during the 2015 summer monsoon have been publically released (http://dx.doi.org/10.3133/ofr20151142) for use by in-country and international agencies.

  19. Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations

    Directory of Open Access Journals (Sweden)

    Lees Jonathan G

    2008-01-01

    Full Text Available Abstract Background A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular dichroism, and infrared spectroscopic data using empirical analysis methods. It has been proposed that comparable accuracy can be obtained from sequence-based predictions as from these biophysical measurements. Here we have examined the secondary structure determination accuracies of sequence prediction methods with the empirically determined values from the spectroscopic data on datasets of proteins for which both crystal structures and spectroscopic data are available. Results In this study we show that the sequence prediction methods have accuracies nearly comparable to those of spectroscopic methods. However, we also demonstrate that combining the spectroscopic and sequences techniques produces significant overall improvements in secondary structure determinations. In addition, combining the extra information content available from synchrotron radiation circular dichroism data with sequence methods also shows improvements. Conclusion Combining sequence prediction with experimentally determined spectroscopic methods for protein secondary structure content significantly enhances the accuracy of the overall results obtained.

  20. Long-PCR based next generation sequencing of the whole mitochondrial genome of the peacock skate Pavoraja nitida (Elasmobranchii: Arhynchobatidae).

    Science.gov (United States)

    Yang, Lei; Naylor, Gavin J P

    2016-01-01

    We determined the complete mitochondrial genome sequence (16,760 bp) of the peacock skate Pavoraja nitida using a long-PCR based next generation sequencing method. It has 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region in the typical vertebrate arrangement. Primers, protocols, and procedures used to obtain this mitogenome are provided. We anticipate that this approach will facilitate rapid collection of mitogenome sequences for studies on phylogenetic relationships, population genetics, and conservation of cartilaginous fishes. PMID:24938110

  1. Direct and crossover PCR amplification to facilitate Tn5supF-based sequencing of lambda phage clones.

    OpenAIRE

    Krishnan, B R; Kersulyte, D; Brikun, I; Berg, C M; Berg, D E

    1991-01-01

    The 264 bp mini-transposon Tn5supF was constructed to sequence DNAs cloned in phage lambda without extensive shotgun subcloning or primer walking. Unique sequences near each transposon end serve as primer binding sites, and a supF gene is used to select transposition to lambda. We describe here PCR methods that facilitate Tn5supF-based sequencing. In a first pass, insertions are mapped relative to the ends of the cloned fragment using pairs of primers specific for vector DNA next to the cloni...

  2. Final Technical Report on the Genome Sequence DataBase (GSDB): DE-FG03 95 ER 62062 September 1997-September 1999; FINAL

    International Nuclear Information System (INIS)

    Since September 1997 NCGR has produced two web-based tools for researchers to use to access and analyze data in the Genome Sequence DataBase (GSDB). These tools are: Sequence Viewer, a nucleotide sequence and annotation visualization tool, and MAR-Finder, a tool that predicts, base upon statistical inferences, the location of matrix attachment regions (MARS) within a nucleotide sequence.[The annual report for June 1996 to August 1997 is included as an attachment to this final report.

  3. Final Technical Report on the Genome Sequence DataBase (GSDB): DE-FG03 95 ER 62062 September 1997-September 1999

    Energy Technology Data Exchange (ETDEWEB)

    Harger, Carol A.

    1999-10-28

    Since September 1997 NCGR has produced two web-based tools for researchers to use to access and analyze data in the Genome Sequence DataBase (GSDB). These tools are: Sequence Viewer, a nucleotide sequence and annotation visualization tool, and MAR-Finder, a tool that predicts, base upon statistical inferences, the location of matrix attachment regions (MARS) within a nucleotide sequence. [The annual report for June 1996 to August 1997 is included as an attachment to this final report.

  4. An improved spectral performance of SPWM inverter based on the time-sequence of chaos

    Institute of Scientific and Technical Information of China (English)

    LI Guan-lin; CHEN Xi-you; LIU Hong-chen; YANG Wei

    2007-01-01

    A novel approach for improving the spectral performance of sinusoidal Pulse Width Modulation (SPWM) inverter is presented. By varying the carrier frequency according to chaotic time-sequence, the discrete spectrum of the output voltage is transformed into the continuous spectrum, which could reduce the acoustic noise concentrated at specific tones in an inverter-driven electric machine. Fourier analysis shows that the harmonic at the fixed frequency has been restrained effectively and the distribution of the spectrum is in a wider range. Besides, a novel variable is introduced for the evaluation of the output voltage spectrum in SPWM inverter. Simulations and experiments with DSP confirm the advantages of the novel approach. Experimental results show the annoying acoustic noise has been translated into some enjoyable sound like a fall or water flowing when this novel method is applied.

  5. Online Detection Approach for Rectangle Ceramic Tile Based on Sequenced Scenery Image

    Directory of Open Access Journals (Sweden)

    Yang Lei

    2013-06-01

    Full Text Available Image based ceramic tile detection is a way to labor liberation in the production process of ceramic tile. Shapes of ceramic tiles studied in this study are rectangle with different sizes. Many existed researches are based on a situation that only a piece of tile goes through special rail one time, resulting in one or less piece of tile hold in the image from CCD sensor. But in fact, multiple tiles with the same sizes run in a row simultaneously at most factories’ rails, and a 'scenery' image is obtained from CCD sensor. And the image processing method based on close-up images is not satisfied in such cases. To detect different rectangle ceramic tiles online according to a sequence of scenery images, this study provide a vector corner method to decide the rectangle tiles with known size information, and a valley detection method via key-image-frames strategy to distinguish the first row in images. Finally, our Online Approach for Rectangle Tile Detection (OARTD was embedded into a detection system and applied to a factory; testing results validated its good performance. Indeed, the use of such an automatic system, to control a tile plant for shape classifying has a good prospect.

  6. Face Recognition from Still Images to Video Sequences: A Local-Feature-Based Framework

    Directory of Open Access Journals (Sweden)

    Chen Shaokang

    2011-01-01

    Full Text Available Although automatic faces recognition has shown success for high-quality images under controlled conditions, for video-based recognition it is hard to attain similar levels of performance. We describe in this paper recent advances in a project being undertaken to trial and develop advanced surveillance systems for public safety. In this paper, we propose a local facial feature based framework for both still image and video-based face recognition. The evaluation is performed on a still image dataset LFW and a video sequence dataset MOBIO to compare 4 methods for operation on feature: feature averaging (Avg-Feature, Mutual Subspace Method (MSM, Manifold to Manifold Distance (MMS, and Affine Hull Method (AHM, and 4 methods for operation on distance on 3 different features. The experimental results show that Multi-region Histogram (MRH feature is more discriminative for face recognition compared to Local Binary Patterns (LBP and raw pixel intensity. Under the limitation on a small number of images available per person, feature averaging is more reliable than MSM, MMD, and AHM and is much faster. Thus, our proposed framework—averaging MRH feature is more suitable for CCTV surveillance systems with constraints on the number of images and the speed of processing.

  7. Blind Demodulation of Chaotic Direct Sequence Spread Spectrum Signals Based on Particle Filters

    Directory of Open Access Journals (Sweden)

    Yimeng Zhang

    2013-09-01

    Full Text Available Applying the particle filter (PF technique, this paper proposes a PF-based algorithm to blindly demodulate the chaotic direct sequence spread spectrum (CDS-SS signals under the colored or non-Gaussian noises condition. To implement this algorithm, the PFs are modified by (i the colored or non-Gaussian noises are formulated by autoregressive moving average (ARMA models, and then the parameters that model the noises are included in the state vector; (ii the range-differentiating factor is imported into the intruder’s chaotic system equation. Since the range-differentiating factor is able to make the inevitable chaos fitting error advantageous based on the chaos fitting method, thus the CDS-SS signals can be demodulated according to the range of the estimated message. Simulations show that the proposed PF-based algorithm can obtain a good bit-error rate performance when extracting the original binary message from the CDS-SS signals without any knowledge of the transmitter’s chaotic map, or initial value, even when colored or non-Gaussian noises exist.

  8. PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

    OpenAIRE

    Kessy Abarenkov; Leho Tedersoo; R Henrik Nilsson; Kai Vellak; Irja Saar; Vilmar Veldre; Erast Parmasto; Marko Prous; Anne Aan; Margus Ots; Olavi Kurina; Ivika Ostonen; Janno Jõgeva; Siim Halapuu; Kadri Põldmaa

    2010-01-01

    DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in...

  9. Prosystemin identification in Amaranthus cruentus and A. hypochondriacus x hybridus based on data mining and sequence alignment

    OpenAIRE

    Žiarovska Jana; Zahorsky Michal; Hricova Andrea

    2016-01-01

    Bioinformatic tool have became an inevitable part of molecular genetic research in many applications. In the present study, an in silico based approach was used to find conservative region of currently known prosystemin gene sequences and its PCR identification was performed in Amaranthus cruentus and Amaranthus hypochondriacus x hybridus. Identification results were veryfied by direct sequencing of obtained amplicons. For both of analysed species, the pros...

  10. Improvement of avian leukosis virus (ALV)-based retrovirus vectors by using different cis-acting sequences from ALVs.

    OpenAIRE

    Cosset, F L; Legras, C.; Thomas, J.L.; Molina, R. M.; Chebloune, Y; Faure, C.; Nigon, V M; Verdier, G

    1991-01-01

    Production and expression of double-expression vectors which transduce both Neo(r) and lacZ genes and are based on the structure of avian leukosis virus were enhanced by using cis-acting sequences (long terminal repeats and noncoding sequences) from Rous-associated virus-1 and Rous-associated virus-2 rather than those of avian erythroblastosis virus previously used in our constructs. Polyclonal producer cells obtained after transfection of these vectors into the Isolde packaging cell line gav...

  11. Effect of k-tuple length on sample-comparison with high-throughput sequencing data.

    Science.gov (United States)

    Wang, Ying; Lei, Xiaoye; Wang, Shun; Wang, Zicheng; Song, Nianfeng; Zeng, Feng; Chen, Ting

    2016-01-22

    The high-throughput metagenomic sequencing offers a powerful technique to compare the microbial communities. Without requiring extra reference sequences, alignment-free models with short k-tuple (k = 2-10 bp) yielded promising results. Short k-tuples describe the overall statistical distribution, but is hard to capture the specific characteristics inside one microbial community. Longer k-tuple contains more abundant information. However, because the frequency vector of long k-tuple(k ≥ 30 bp) is sparse, the statistical measures designed for short k-tuples are not applicable. In our study, we considered each tuple as a meaningful word and then each sequencing data as a document composed of the words. Therefore, the comparison between two sequencing data is processed as "topic analysis of documents" in text mining. We designed a pipeline with long k-tuple features to compare metagenomic samples combined using algorithms from text mining and pattern recognition. The pipeline is available at http://culotuple.codeplex.com/. Experiments show that our pipeline with long k-tuple features: ①separates genomes with high similarity; ②outperforms short k-tuple models in all experiments. When k ≥ 12, the short k-tuple measures are not applicable anymore. When k is between 20 and 40, long k-tuple pipeline obtains much better grouping results; ③is free from the effect of sequencing platforms/protocols. ③We obtained meaningful and supported biological results on the 40-tuples selected for comparison. PMID:26721429

  12. Phylogeny of Populus (Salicaceae) based on nucleotide sequences of chloroplast TRNT-TRNF region and nuclear rDNA.

    Science.gov (United States)

    Hamzeh, Mona; Dayanandan, Selvadurai

    2004-09-01

    The species of the genus Populus, collectively known as poplars, are widely distributed over the northern hemisphere and well known for their ecological, economical, and evolutionary importance. The extensive interspecific hybridization and high morphological diversity in this group pose difficulties in identifying taxonomic units for comparative evolutionary studies and systematics. To understand the evolutionary relationships among poplars and to provide a framework for biosystematic classification, we reconstructed a phylogeny of the genus Populus based on nucleotide sequences of three noncoding regions of the chloroplast DNA (intron of trnL and intergenic regions of trnT-trnL and trnL-trnF) and ITS1 and ITS2 of the nuclear rDNA. The resulting phylogenetic trees showed polyphyletic relationships among species in the sections Tacamahaca and Aigeiros. Based on chloroplast DNA sequence data, P. nigra had a close affinity to species of section Populus, whereas nuclear DNA sequence data suggested a close relationship between P. nigra and species of the section Aigeiros, suggesting a possible hybrid origin for P. nigra. Similarly, the chloroplast DNA sequences of P. tristis and P. szechuanica were similar to that of the species of section Aigeiros, while the nuclear sequences revealed a close affinity to species of the section Tacamahaca, suggesting a hybrid origin for these two Asiatic balsam poplars. The incongruence between phylogenetic trees based on nuclear- and chloroplast-DNA sequence data suggests a reticulate evolution in the genus Populus. PMID:21652373

  13. Effect of long-term idle periods on the performance of sequencing batch reactors

    DEFF Research Database (Denmark)

    Morgenroth, Eberhard Friedrich; Obermayer, A.; Arnold, E.; Brühl, A.; Wagner, M.; Wilderer, P. A.

    2000-01-01

    Sludge storage can be used as an effective control handle to adjust plant capacity to large influent variations. The sequencing batch reactor (SBR) technology is well suited for temporary sludge storage because reactors can easily be switched off individually and operated in an idle mode. In this...... study experimental results on the effect of long term (weeks) idle periods on nitrogen removal are presented. The SBRs were operated with idle times ranging from 6 to 20 days. Batch experiments were performed where sludge was stored without the addition of any substrate for 7 weeks. In the SBRs...

  14. The effect of sequence repeat time on auditory cortex stimulation during phonetic discrimination

    OpenAIRE

    Shah, J. N.; Steinhoff, S; Mirzazade, S.; Zafiris, O.; Grosse-Ruyken, M. L.; Jäncke, R. K.; Zilles, K

    2000-01-01

    Acoustic noise generated by the MR scanner gradient system during fMRI studies of auditory function is a very significant potential confound. Despite these deleterious effects, fMRI of the auditory cortex has been successful and numerous practitioners have circumvented the problem of acoustic masking noise. In the context of auditory cortex fMRI, the sequence repeat time (TR) has the effect of altering the length of time during which the scanner is quiet. Indeed, the move to whole-brain fMRI ...

  15. Transcriptome walking: a laboratory-oriented GUI-based approach to mRNA identification from deep-sequenced data

    Directory of Open Access Journals (Sweden)

    French Andrew S

    2012-12-01

    Full Text Available Abstract Background Deep sequencing technology provides efficient and economical production of large numbers of randomly positioned, relatively short, estimates of base identities in DNA molecules. Application of this technology to mRNA samples allows rapid examination of the molecular genetic environment in individual cells or tissues, the transcriptome. However, assembly of such short sequences into complete mRNA creates a challenge that limits the usefulness of the technology, particularly when no, or limited, genomic data is available. Several approaches to this problem have been developed, but there is still no general method to rapidly obtain an mRNA sequence from deep sequence data when a specific molecule, or family of molecules, are of interest. A frequent requirement is to identify specific mRNA molecules from tissues that are being investigated by methods such as electrophysiology, immunocytology and pharmacology. To be widely useful, any approach must be relatively simple to use in the laboratory by operators without extensive statistical or bioinformatics knowledge, and with readily available hardware. Findings An approach was developed that allows de novo assembly of individual mRNA sequences in two linked stages: sequence discovery and sequence completion. Both stages rely on computer assisted, Graphical User Interface (GUI-guided, user interaction with the data, but proceed relatively efficiently once discovery is complete. The method grows a discovered sequence by repeated passes through the complete raw data in a series of steps, and is hence termed ‘transcriptome walking’. All of the operations required for transcriptome analysis are combined in one program that presents a relatively simple user interface and runs on a standard desktop, or laptop computer, but takes advantage of multi-core processors, when available. Complete mRNA sequence identifications usually require less than 24 hours. This approach has already

  16. Welding sequence effects on residual stress distribution in offshore wind monopile structures

    Directory of Open Access Journals (Sweden)

    Ali Mehmanparast

    2016-01-01

    Full Text Available Residual stresses are often inevitably introduced into the material during the fabrication processes, such as welding, and are known to have significant effects on the subsequent fatigue crack growth behavior of welded structures. In this paper, the importance of welding sequence on residual stress distribution in engineering components has been reviewed. In addition, the findings available in the literature have been used to provide an accurate interpretation of the fatigue crack growth data on specimens extracted from the welded plates employed in offshore wind monopile structures. The results have been discussed in terms of the role of welding sequence in damage inspection and structural integrity assessment of offshore renewable energy structures.

  17. Effects of RNA sequence specificity in the electrostatic stabilization of viruses

    CERN Document Server

    Erdemci-Tandogan, Gonca; van der Schoot, Paul; Podgornik, Rudolf; Zandi, Roya

    2016-01-01

    Many single-stranded (ss) RNA viruses self assemble from capsid protein subunits and the nucleic acid to form an infectious virion. It is believed that the electrostatic interactions between the negatively charged RNA and the positively charged viral capsid proteins drive the encapsidation, although there is growing evidence that the sequence of the viral RNA also plays a role in packaging. In particular the sequence will determine the possible secondary structures that the ssRNA will take in solution. In this work, we use a mean field theory to investigate how the secondary structure of the RNA combined with electrostatic interactions affects the efficiency of assembly and stability of the assembled virions. We show that the secondary structure of RNA may result in negative osmotic pressures while a linear polymer causes positive osmotic pressures for the same conditions. This may suggest that the branched structure makes the RNA more effectively packaged and the virion more stable.

  18. GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization

    Directory of Open Access Journals (Sweden)

    Ranjan Akash

    2007-08-01

    Full Text Available Abstract Background Mycobacterium smegmatis is fast growing non-pathogenic mycobacteria. This organism has been widely used as a model organism to study the biology of other virulent and extremely slow growing species like Mycobacterium tuberculosis. Based on the homology of the N-terminal DNA binding domain, the recently sequenced genome of M. smegmatis has been shown to possess several putative GntR regulators. A striking characteristic feature of this family of regulators is that they possess a conserved N-terminal DNA binding domain and a diverse C-terminal domain involved in the effector binding and/or oligomerization. Since the physiological role of these regulators is critically dependent upon effector binding and operator sites, we have analysed and classified these regulators into their specific subfamilies and identified their potential binding sites. Results The sequence analysis of M. smegmatis putative GntRs has revealed that FadR, HutC, MocR and the YtrA-like regulators are encoded by 45, 8, 8 and 1 genes respectively. Further out of 45 FadR-like regulators, 19 were classified into the FadR group and 26 into the VanR group. All these proteins showed similar secondary structural elements specific to their respective subfamilies except MSMEG_3959, which showed additional secondary structural elements. Using the reciprocal BLAST searches, we further identified the orthologs of these regulators in Bacillus subtilis and other mycobacteria. Since the expression of many regulators is auto-regulatory, we have identified potential operator sites for a number of these GntR regulators by analyzing the upstream sequences. Conclusion This study helps in extending the annotation of M. smegmatis GntR proteins. It identifies the GntR regulators of M. smegmatis that could serve as a model for studying orthologous regulators from virulent as well as other saprophytic mycobacteria. This study also sheds some light on the nucleotide preferences in the

  19. Deciphering Clostridium tyrobutyricum Metabolism Based on the Whole-Genome Sequence and Proteome Analyses

    Science.gov (United States)

    Lee, Joungmin; Jang, Yu-Sin; Han, Mee-Jung; Kim, Jin Young

    2016-01-01

    ABSTRACT Clostridium tyrobutyricum is a Gram-positive anaerobic bacterium that efficiently produces butyric acid and is considered a promising host for anaerobic production of bulk chemicals. Due to limited knowledge on the genetic and metabolic characteristics of this strain, however, little progress has been made in metabolic engineering of this strain. Here we report the complete genome sequence of C. tyrobutyricum KCTC 5387 (ATCC 25755), which consists of a 3.07-Mbp chromosome and a 63-kbp plasmid. The results of genomic analyses suggested that C. tyrobutyricum produces butyrate from butyryl-coenzyme A (butyryl-CoA) through acetate reassimilation by CoA transferase, differently from Clostridium acetobutylicum, which uses the phosphotransbutyrylase-butyrate kinase pathway; this was validated by reverse transcription-PCR (RT-PCR) of related genes, protein expression levels, in vitro CoA transferase assay, and fed-batch fermentation. In addition, the changes in protein expression levels during the course of batch fermentations on glucose were examined by shotgun proteomics. Unlike C. acetobutylicum, the expression levels of proteins involved in glycolytic and fermentative pathways in C. tyrobutyricum did not decrease even at the stationary phase. Proteins related to energy conservation mechanisms, including Rnf complex, NfnAB, and pyruvate-phosphate dikinase that are absent in C. acetobutylicum, were identified. Such features explain why this organism can produce butyric acid to a much higher titer and better tolerate toxic metabolites. This study presenting the complete genome sequence, global protein expression profiles, and genome-based metabolic characteristics during the batch fermentation of C. tyrobutyricum will be valuable in designing strategies for metabolic engineering of this strain. PMID:27302759

  20. Knowledge-based decision support for Space Station assembly sequence planning

    Science.gov (United States)

    1991-04-01

    A complete Personal Analysis Assistant (PAA) for Space Station Freedom (SSF) assembly sequence planning consists of three software components: the system infrastructure, intra-flight value added, and inter-flight value added. The system infrastructure is the substrate on which software elements providing inter-flight and intra-flight value-added functionality are built. It provides the capability for building representations of assembly sequence plans and specification of constraints and analysis options. Intra-flight value-added provides functionality that will, given the manifest for each flight, define cargo elements, place them in the National Space Transportation System (NSTS) cargo bay, compute performance measure values, and identify violated constraints. Inter-flight value-added provides functionality that will, given major milestone dates and capability requirements, determine the number and dates of required flights and develop a manifest for each flight. The current project is Phase 1 of a projected two phase program and delivers the system infrastructure. Intra- and inter-flight value-added were to be developed in Phase 2, which has not been funded. Based on experience derived from hundreds of projects conducted over the past seven years, ISX developed an Intelligent Systems Engineering (ISE) methodology that combines the methods of systems engineering and knowledge engineering to meet the special systems development requirements posed by intelligent systems, systems that blend artificial intelligence and other advanced technologies with more conventional computing technologies. The ISE methodology defines a phased program process that begins with an application assessment designed to provide a preliminary determination of the relative technical risks and payoffs associated with a potential application, and then moves through requirements analysis, system design, and development.

  1. A stochastic context free grammar based framework for analysis of protein sequences

    Directory of Open Access Journals (Sweden)

    Nebel Jean-Christophe

    2009-10-01

    Full Text Available Abstract Background In the last decade, there have been many applications of formal language theory in bioinformatics such as RNA structure prediction and detection of patterns in DNA. However, in the field of proteomics, the size of the protein alphabet and the complexity of relationship between amino acids have mainly limited the application of formal language theory to the production of grammars whose expressive power is not higher than stochastic regular grammars. However, these grammars, like other state of the art methods, cannot cover any higher-order dependencies such as nested and crossing relationships that are common in proteins. In order to overcome some of these limitations, we propose a Stochastic Context Free Grammar based framework for the analysis of protein sequences where grammars are induced using a genetic algorithm. Results This framework was implemented in a system aiming at the production of binding site descriptors. These descriptors not only allow detection of protein regions that are involved in these sites, but also provide insight in their structure. Grammars were induced using quantitative properties of amino acids to deal with the size of the protein alphabet. Moreover, we imposed some structural constraints on grammars to reduce the extent of the rule search space. Finally, grammars based on different properties were combined to convey as much information as possible. Evaluation was performed on sites of various sizes and complexity described either by PROSITE patterns, domain profiles or a set of patterns. Results show the produced binding site descriptors are human-readable and, hence, highlight biologically meaningful features. Moreover, they achieve good accuracy in both annotation and detection. In addition, findings suggest that, unlike current state-of-the-art methods, our system may be particularly suited to deal with patterns shared by non-homologous proteins. Conclusion A new Stochastic Context Free

  2. Rapid Detection and Identification of Infectious Pathogens Based on High-throughput Sequencing

    Directory of Open Access Journals (Sweden)

    Pei-Xiang Ni

    2015-01-01

    Full Text Available Background: The dilemma of pathogens identification in patients with unidentified clinical symptoms such as fever of unknown origin exists, which not only poses a challenge to both the diagnostic and therapeutic process by itself, but also to expert physicians. Methods: In this report, we have attempted to increase the awareness of unidentified pathogens by developing a method to investigate hitherto unidentified infectious pathogens based on unbiased high-throughput sequencing. Results: Our observations show that this method supplements current diagnostic technology that predominantly relies on information derived five cases from the intensive care unit. This methodological approach detects viruses and corrects the incidence of false positive detection rates of pathogens in a much shorter period. Through our method is followed by polymerase chain reaction validation, we could identify infection with Epstein-Barr virus, and in another case, we could identify infection with Streptococcus viridians based on the culture, which was false positive. Conclusions: This technology is a promising approach to revolutionize rapid diagnosis of infectious pathogens and to guide therapy that might result in the improvement of personalized medicine.

  3. Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach.

    Directory of Open Access Journals (Sweden)

    Alexander Eiler

    Full Text Available The recognition and discrimination of phytoplankton species is one of the foundations of freshwater biodiversity research and environmental monitoring. This step is frequently a bottleneck in the analytical chain from sampling to data analysis and subsequent environmental status evaluation. Here we present phytoplankton diversity data from 49 lakes including three seasonal surveys assessed by next generation sequencing (NGS of 16S ribosomal RNA chloroplast and cyanobacterial gene amplicons and also compare part of these datasets with identification based on morphology. Direct comparison of NGS to microscopic data from three time-series showed that NGS was able to capture the seasonality in phytoplankton succession as observed by microscopy. Still, the PCR-based approach was only semi-quantitative, and detailed NGS and microscopy taxa lists had only low taxonomic correspondence. This is probably due to, both, methodological constraints and current discrepancies in taxonomic frameworks. Discrepancies included Euglenophyta and Heterokonta that were scarce in the NGS but frequently detected by microscopy and Cyanobacteria that were in general more abundant and classified with high resolution by NGS. A deep-branching taxonomically unclassified cluster was frequently detected by NGS but could not be linked to any group identified by microscopy. NGS derived phytoplankton composition differed significantly among lakes with different trophic status, showing that our approach can resolve phytoplankton communities at a level relevant for ecosystem management. The high reproducibility and potential for standardization and parallelization makes our NGS approach an excellent candidate for simultaneous monitoring of prokaryotic and eukaryotic phytoplankton in inland waters.

  4. Evaluation of Superimposed Sequence Components of Currents based Islanding Detection Scheme during DG Interconnections

    Science.gov (United States)

    Sareen, Karan; Bhalja, Bhavesh R.; Maheshwari, Rudra Prakash

    2016-02-01

    A new islanding detection scheme for distribution network containing different types of distributed generations (DGs) is presented in this paper. The proposed scheme is based on acquiring three phase current samples for full cycle duration of each simulation case of islanding/non-islanding conditions at the point of common coupling (PCC) of the targeted DG. Afterwards, superimposed positive & negative sequence components of current are calculated and continuously compared with pre-determined threshold values. Performance of the proposed scheme has been evaluated on diversified islanding and non-islanding events which were generated by modeling standard IEEE 34-bus system using PSCAD/EMTDC software package. The proposed scheme is capable to detect islanding condition rapidly even for perfect power balance situation for both synchronous and inverter based DGs. Furthermore, it remains stable during non-islanding events such as tripping of multiple DGs and different DG interconnection operating conditions. Therefore, the proposed scheme avoids nuisance tripping during diversified non-islanding events. At the end, comparison of the proposed scheme with the existing scheme clearly indicates its advantage over the existing scheme.

  5. Eliciting neutralizing antibodies with gp120 outer domain constructs based on M-group consensus sequence.

    Science.gov (United States)

    Qin, Yali; Banasik, Marisa; Kim, SoonJeung; Penn-Nicholson, Adam; Habte, Habtom H; LaBranche, Celia; Montefiori, David C; Wang, Chong; Cho, Michael W

    2014-08-01

    One strategy being evaluated for HIV-1 vaccine development is focusing immune responses towards neutralizing epitopes on the gp120 outer domain (OD) by removing the immunodominant, but non-neutralizing, inner domain. Previous OD constructs have not elicited strong neutralizing antibodies (nAbs). We constructed two immunogens, a monomeric gp120-OD and a trimeric gp120-OD×3, based on an M group consensus sequence (MCON6). Their biochemical and immunological properties were compared with intact gp120. Results indicated better preservation of critical neutralizing epitopes on gp120-OD×3. In contrast to previous studies, our immunogens induced potent, cross-reactive nAbs in rabbits. Although nAbs primarily targeted Tier 1 viruses, they exhibited significant breadth. Epitope mapping analyses indicated that nAbs primarily targeted conserved V3 loop elements. Although the potency and breadth of nAbs were similar for all three immunogens, nAb induction kinetics indicated that gp120-OD×3 was superior to gp120-OD, suggesting that gp120-OD×3 is a promising prototype for further gp120 OD-based immunogen development. PMID:25046154

  6. Design and implementation of microcontroller-based automatic sequence counting and switching system

    Directory of Open Access Journals (Sweden)

    Joshua ABOLARINWA

    2015-05-01

    Full Text Available Technological advancement and its influence on human being have been on the increase in recent time. Major areas of such influence, include monitoring and control activities. In order to keep track of human movement in and out of a particular building, there is the need for an automatic counting system. Therefore, in this paper, we present the design and implementation of a microcontroller-based automatic sequence counting and switching system. This system was designed and developed to save cost, time, energy, and to achieve seamless control in the event of switching on or off of electrical appliances within a building. Top-down modular design approach was used in conjunction with the versatility of microcontroller. The system is able to monitor, sequentially count the number of entry and exit of people through an entrance, afterwards, automatically control any electrical device connected to it. From various tests and measurements obtained, there are comparative benefits derived from the deployment of this system in terms of simplicity and accuracy over similar system that is not microcontroller-based. Therefore, this system can be deployed at commercial quantity with wide range of applications in homes, offices and other public places.

  7. Modular robotic intelligence system based on fuzzy reasoning and state machine sequencing

    Science.gov (United States)

    Sights, B.; Ahuja, G.; Kogut, G.; Pacis, E. B.; Everett, H. R.; Fellars, D.; Hardjadinata, S.

    2007-04-01

    The fusion of multiple behavior commands and sensor data into intelligent and cohesive robotic movement has been the focus of robot research for many years. Sequencing low level behaviors to create high level intelligence has also been researched extensively. Cohesive robotic movement is also dependent on other factors, such as environment, user intent, and perception of the environment. In this paper, a method for managing the complexity derived from the increase in sensors and perceptions is described. Our system uses fuzzy logic and a state machine to fuse multiple behaviors into an optimal response based on the robot's current task. The resulting fused behavior is filtered through fuzzy logic based obstacle avoidance to create safe movement. The system also provides easy integration with any communications protocol, plug-and-play devices, perceptions, and behaviors. Most behaviors and the obstacle avoidance parameters are easily changed through configuration files. Combined with previous work in the area of navigation and localization a very robust autonomy suite is created.

  8. A sequence-based genetic linkage map as a reference for Brassica rapa pseudochromosome assembly

    OpenAIRE

    Cheng Feng; Wang Qian; Liao Yongcui; Deng Jie; Wang Hui(Wendy); Liu Bo; Sun Silong; Wang Yan; Wang Xiaowu; Wu Jian

    2011-01-01

    Abstract Background Brassica rapa is an economically important crop and a model plant for studies concerning polyploidization and the evolution of extreme morphology. The multinational B. rapa Genome Sequencing Project (BrGSP) was launched in 2003. In 2008, next generation sequencing technology was used to sequence the B. rapa genome. Several maps concerning B. rapa pseudochromosome assembly have been published but their coverage of the genome is incomplete, anchoring approximately 73.6% of t...

  9. Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.

    Directory of Open Access Journals (Sweden)

    Jonathan Z Li

    Full Text Available The impact of raltegravir-resistant HIV-1 minority variants (MVs on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs.A5262 was a single-arm study of raltegravir and darunavir/ritonavir in treatment-naïve patients. Pre-treatment plasma was obtained from 5 participants with raltegravir resistance at the time of virologic failure. A control library was created by pooling integrase clones at predefined proportions. Multiplexed sequencing was performed with Illumina and 454 platforms at comparable costs. Illumina sequence analysis was performed with the novel snp-assess tool and 454 sequencing was analyzed with V-Phaser.Illumina sequencing resulted in significantly higher sequence coverage and a 0.095% limit of detection. Illumina accurately detected all MVs in the control library at ≥0.5% and 7/10 MVs expected at 0.1%. 454 sequencing failed to detect any MVs at 0.1% with 5 false positive calls. For MVs detected in the patient samples by both 454 and Illumina, the correlation in the detected variant frequencies was high (R2 = 0.92, P<0.001. Illumina sequencing detected 2.4-fold greater nucleotide MVs and 2.9-fold greater amino acid MVs compared to 454. The only raltegravir-resistant MV detected was an E138K mutation in one participant by Illumina sequencing, but not by 454.In participants of A5262 with raltegravir resistance at virologic failure, baseline raltegravir-resistant MVs were rarely detected. At comparable costs to 454 sequencing, Illumina demonstrated greater depth of coverage, increased sensitivity for detecting HIV MVs, and fewer false positive variant calls.

  10. Comparison of Illumina and 454 Deep Sequencing in Participants Failing Raltegravir-Based Antiretroviral Therapy

    OpenAIRE

    Li, Jonathan Z.; Chapman, Brad; Charlebois, Patrick; Hofmann, Oliver; Weiner, Brian; Porter, Alyssa J.; Samuel, Reshmi; Vardhanabhuti, Saran; ZHENG, LU; Eron, Joseph; Taiwo, Babafemi; Zody, Michael C; Henn, Matthew R.; Daniel R Kuritzkes; Hide, Winston

    2014-01-01

    Background: The impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs. Methods: A5262 was a single-arm study of raltegravir and darunavir/ritonavir in treatment-naïve patients. Pre-treatment plasma was obtained from 5 participants with raltegra...

  11. Comparison of Illumina and 454 Deep Sequencing in Participants Failing Raltegravir-Based Antiretroviral Therapy

    OpenAIRE

    Li, Jonathan Z.; Brad Chapman; Patrick Charlebois; Oliver Hofmann; Brian Weiner; Porter, Alyssa J.; Reshmi Samuel; Saran Vardhanabhuti; Lu Zheng; Joseph Eron; Babafemi Taiwo; Zody, Michael C; Henn, Matthew R.; Daniel R Kuritzkes; Winston Hide

    2014-01-01

    BACKGROUND: The impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs. METHODS: A5262 was a single-arm study of raltegravir and darunavir/ritonavir in treatment-naïve patients. Pre-treatment plasma was obtained from 5 participants with raltegra...

  12. MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

    OpenAIRE

    Lee, Wan-Ping; Stromberg, Michael P.; Ward, Alistair; Stewart, Chip; Garrison, Erik P.; Marth, Gabor T.

    2014-01-01

    MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the ...

  13. A novel all-optical label processing for OPS networks based on multiple OOC sequences from multiple-groups OOC

    Science.gov (United States)

    Qiu, Kun; Zhang, Chongfu; Ling, Yun; Wang, Yibo

    2007-11-01

    This paper proposes an all-optical label processing scheme using multiple optical orthogonal codes sequences (MOOCS) for optical packet switching (OPS) (MOOCS-OPS) networks, for the first time to the best of our knowledge. In this scheme, the multiple optical orthogonal codes (MOOC) from multiple-groups optical orthogonal codes (MGOOC) are permuted and combined to obtain the MOOCS for the optical labels, which are used to effectively enlarge the capacity of available optical codes for optical labels. The optical label processing (OLP) schemes are reviewed and analyzed, the principles of MOOCS-based optical labels for OPS networks are given, and analyzed, then the MOOCS-OPS topology and the key realization units of the MOOCS-based optical label packets are studied in detail, respectively. The performances of this novel all-optical label processing technology are analyzed, the corresponding simulation is performed. These analysis and results show that the proposed scheme can overcome the lack of available optical orthogonal codes (OOC)-based optical labels due to the limited number of single OOC for optical label with the short code length, and indicate that the MOOCS-OPS scheme is feasible.

  14. Classifying Genomic Sequences by Sequence Feature Analysis

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hua Liu; Dian Jiao; Xiao Sun

    2005-01-01

    Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream,exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis.

  15. The Effects of Meiosis/Genetics Integration and Instructional Sequence on College Biology Student Achievement in Genetics.

    Science.gov (United States)

    Browning, Mark

    The purpose of the research was to manipulate two aspects of genetics instruction in order to measure their effects on college, introductory biology students' achievement in genetics. One instructional sequence that was used dealt first with monohybrid autosomal inheritance patterns, then sex-linkage. The alternate sequence was the reverse.…

  16. The Ubiquitous Nature of the Hebb Repetition Effect: Error Learning Mistaken for the Absence of Sequence Learning

    Science.gov (United States)

    Lafond, Daniel; Tremblay, Sebastien; Parmentier, Fabrice

    2010-01-01

    Sequence learning is essential in cognition and underpins activities such as language and skill acquisition. One classical demonstration of sequence learning is that of the Hebb repetition effect, whereby serial recall improves over repetitions on a repeated list relative to random lists. When addressing the question of which mechanism underlies…

  17. Effects of "D"-Amphetamine and Ethanol on Variable and Repetitive Key-Peck Sequences in Pigeons

    Science.gov (United States)

    Ward, Ryan D.; Bailey, Ericka M.; Odum, Amy L.

    2006-01-01

    This experiment assessed the effects of "d"-Amphetamine and ethanol on reinforced variable and repetitive key-peck sequences in pigeons. Pigeons responded on two keys under a multiple schedule of Repeat and Vary components. In the Repeat component, completion of a target sequence of right, right, left, left resulted in food. In the Vary component,…

  18. Effect of single-point sequence alterations on the aggregationpropensity of a model protein

    Energy Technology Data Exchange (ETDEWEB)

    Bratko, Dusan; Cellmer, Troy; Prausnitz, John M.; Blanch, Harvey W.

    2005-10-07

    Sequences of contemporary proteins are believed to have evolved through process that optimized their overall fitness including their resistance to deleterious aggregation. Biotechnological processing may expose therapeutic proteins to conditions that are much more conducive to aggregation than those encountered in a cellular environment. An important task of protein engineering is to identify alternative sequences that would protect proteins when processed at high concentrations without altering their native structure associated with specific biological function. Our computational studies exploit parallel tempering simulations of coarse-grained model proteins to demonstrate that isolated amino-acid residue substitutions can result in significant changes in the aggregation resistance of the protein in a crowded environment while retaining protein structure in isolation. A thermodynamic analysis of protein clusters subject to competing processes of folding and association shows that moderate mutations can produce effects similar to those caused by changes in system conditions, including temperature, concentration, and solvent composition that affect the aggregation propensity. The range of conditions where a protein can resist aggregation can therefore be tuned by sequence alterations although the protein generally may retain its generic ability for aggregation.

  19. EFFECTS OF 4-CHLOROPHENOL LOADINGS ON ACCLIMATION OF BIOMASS WITH OPTIMIZED FIXED TIME SEQUENCING BATCH REACTOR

    Directory of Open Access Journals (Sweden)

    H. Movahedyan, A. Assadi, M. M. Amin

    2008-10-01

    Full Text Available Abstract: Chlorinated phenols in many industrial effluents are usually difficult to be removed by conventional biological treatment processes. Performance of the aerobic sequencing batch reactor treating 4-chlorophenol containing wastewater at different loadings rates from 0.0075 to 1.2 g4CP/L.d was evaluated. The sequencing batch reactor was operated with fill, react, settle and decant phases in the order of 10:370:90:10 min, respectively, for a cycle time of 8 h at 10 days solid retention time and 16 h hydraulic retention time in the stable period. The effects of 4-chlorophenol loadings on the 4-chlorophenol and chemical oxygen demand removal percents, yield coefficient (Y, biomass variation and sludge volume index were investigated. High chemical oxygen demand removal efficiencies (95±3.5% and approximately complete 4-chlorophenol removal (>99% were observed even in the absence of growth substrate. The degradation of 4-chlorophenol led to formation of 5-chloro-2-hydroxymuconic semialdehyde, which was more oxidized, indicating complete disappearance of 4-chlorophenol via meta-cleavage pathway. A compact sludge with excellent settleability (sludge volume index=47±6.1 mL/g developed during entire acclimation period. High removal efficiencies with sequencing batch reactor may be due to enforced short term unsteady state conditions coupled with periodic exposure of the microorganisms to defined process conditions which facilitate the required metabolic pathways for treating xenobiotics containing wastewater.

  20. Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions.

    Science.gov (United States)

    Liu, Maoyan; Liu, Xiangning; Li, Xun; Zhang, Deyong; Dai, Liangyin; Tang, Qianjun

    2016-03-01

    The genome sequence of pepper vein yellows virus (PeVYV) (PeVYV-HN, accession number KP326573), isolated from pepper plants (Capsicum annuum L.) grown at the Hunan Vegetables Institute (Changsha, Hunan, China), was determined by deep sequencing of small RNAs. The PeVYV-HN genome consists of 6244 nucleotides, contains six open reading frames (ORFs), and is similar to that of an isolate (AB594828) from Japan. Its genomic organization is similar to that of members of the genus Polerovirus. Sequence analysis revealed that PeVYV-HN shared 92% sequence identity with the Japanese PeVYV genome at both the nucleotide and amino acid levels. Evolutionary analysis based on the coat protein (CP), movement protein (MP), and RNA-dependent RNA polymerase (RdRP) showed that PeVYV could be divided into two major lineages corresponding to their geographical origins. The Asian isolates have a higher population expansion frequency than the African isolates. Negative selection and genetic drift (founder effect) were found to be the potential drivers of the molecular evolution of PeVYV. Moreover, recombination was not the distinct cause of PeVYV evolution. This is the first report of a complete genomic sequence of PeVYV in China. PMID:26620586