WorldWideScience

Sample records for alignment search tool

  1. HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool.

    Science.gov (United States)

    O'Driscoll, Aisling; Belogrudov, Vladislav; Carroll, John; Kropp, Kai; Walsh, Paul; Ghazal, Peter; Sleator, Roy D

    2015-04-01

    The recent exponential growth of genomic databases has resulted in the common task of sequence alignment becoming one of the major bottlenecks in the field of computational biology. It is typical for these large datasets and complex computations to require cost prohibitive High Performance Computing (HPC) to function. As such, parallelised solutions have been proposed but many exhibit scalability limitations and are incapable of effectively processing "Big Data" - the name attributed to datasets that are extremely large, complex and require rapid processing. The Hadoop framework, comprised of distributed storage and a parallelised programming framework known as MapReduce, is specifically designed to work with such datasets but it is not trivial to efficiently redesign and implement bioinformatics algorithms according to this paradigm. The parallelisation strategy of "divide and conquer" for alignment algorithms can be applied to both data sets and input query sequences. However, scalability is still an issue due to memory constraints or large databases, with very large database segmentation leading to additional performance decline. Herein, we present Hadoop Blast (HBlast), a parallelised BLAST algorithm that proposes a flexible method to partition both databases and input query sequences using "virtual partitioning". HBlast presents improved scalability over existing solutions and well balanced computational work load while keeping database segmentation and recompilation to a minimum. Enhanced BLAST search performance on cheap memory constrained hardware has significant implications for in field clinical diagnostic testing; enabling faster and more accurate identification of pathogenic DNA in human blood or tissue samples. PMID:25625550

  2. DNA Align Editor: DNA Alignment Editor Tool

    Science.gov (United States)

    The SNPAlignEditor is a DNA sequence alignment editor that runs on Windows platforms. The purpose of the program is to provide an intuitive, user-friendly tool for manual editing of multiple sequence alignments by providing functions for input, editing, and output of nucleotide sequence alignments....

  3. PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability

    OpenAIRE

    Venclovas Česlovas; Margelevičius Mindaugas

    2005-01-01

    Abstract Background Protein sequence alignments have become indispensable for virtually any evolutionary, structural or functional study involving proteins. Modern sequence search and comparison methods combined with rapidly increasing sequence data often can reliably match even distantly related proteins that share little sequence similarity. However, even highly significant matches generally may have incorrectly aligned regions. Therefore when exact residue correspondence is used to transfe...

  4. A cross-species alignment tool (CAT)

    DEFF Research Database (Denmark)

    Li, Heng; Guan, Liang; Liu, Tao;

    2007-01-01

    sensitive methods which are usually applied in aligning inter-species sequences. RESULTS: Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web at...... http://xat.sourceforge.net/. CONCLUSIONS: Examined from different angles, CAT outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that CAT combines the specificity and speed of the best intra-species algorithms, like BLAT and...

  5. Strategies and tools for whole genome alignments

    Energy Technology Data Exchange (ETDEWEB)

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna

    2002-11-25

    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  6. Multiview alignment hashing for efficient image search.

    Science.gov (United States)

    Liu, Li; Yu, Mengyang; Shao, Ling

    2015-03-01

    Hashing is a popular and efficient method for nearest neighbor search in large-scale data spaces by embedding high-dimensional feature descriptors into a similarity preserving Hamming space with a low dimension. For most hashing methods, the performance of retrieval heavily depends on the choice of the high-dimensional feature descriptor. Furthermore, a single type of feature cannot be descriptive enough for different images when it is used for hashing. Thus, how to combine multiple representations for learning effective hashing functions is an imminent task. In this paper, we present a novel unsupervised multiview alignment hashing approach based on regularized kernel nonnegative matrix factorization, which can find a compact representation uncovering the hidden semantics and simultaneously respecting the joint probability distribution of data. In particular, we aim to seek a matrix factorization to effectively fuse the multiple information sources meanwhile discarding the feature redundancy. Since the raised problem is regarded as nonconvex and discrete, our objective function is then optimized via an alternate way with relaxation and converges to a locally optimal solution. After finding the low-dimensional representation, the hashing functions are finally obtained through multivariable logistic regression. The proposed method is systematically evaluated on three data sets: 1) Caltech-256; 2) CIFAR-10; and 3) CIFAR-20, and the results show that our method significantly outperforms the state-of-the-art multiview hashing techniques. PMID:25594968

  7. Strategic alignment: a performance tool for SMEs

    OpenAIRE

    Jouirou, Nihel; Kalika, Michel

    2004-01-01

    The purpose of this research is to investigate whether the alignment of IT with the strategy (particularly the partnership strategy or cooperation practice) and organizational structure of an SME could have a decisive influence on its performance. We constructed a model and tested it empirically using data from 381 SMEs operating in different sectors. A multivariate perspective, modelled with structural equations, was used to test the alignment between strategy, structure and IT. The alignmen...

  8. Report on tool transfer and alignment methods

    DEFF Research Database (Denmark)

    Tosello, Guido; Gasparin, Stefania; De Grave, Arnaud;

    2010-01-01

    In the last few years, research work has been carried out regarding the feature miniaturization and tooling performance achievable with specific process chains combining different micro machining processes. On the other hand, technologies, strategies and tool design rules in order to optimize the...... accuracy of the hybrid tooling process chain with a focus on the part transfer and re-position of different machining chains have not been addressed thoroughly and are the topic of Task 2.2.3 “Tool transfer for hybrid manufacturing”. First results are presented in this report, focussing on a specific...... process chain for tooling (i.e. hybrid tooling) based on the combination of micro milling and micro electrical discharge machining (EDM) milling, both at machine tool and at machining technology levels....

  9. Basic Local Alignment Search Tool (BLAST)

    Data.gov (United States)

    U.S. Department of Health & Human Services — BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the...

  10. Absorber Alignment Measurement Tool for Solar Parabolic Trough Collectors: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Stynes, J. K.; Ihas, B.

    2012-04-01

    As we pursue efforts to lower the capital and installation costs of parabolic trough solar collectors, it is essential to maintain high optical performance. While there are many optical tools available to measure the reflector slope errors of parabolic trough solar collectors, there are few tools to measure the absorber alignment. A new method is presented here to measure the absorber alignment in two dimensions to within 0.5 cm. The absorber alignment is measured using a digital camera and four photogrammetric targets. Physical contact with the receiver absorber or glass is not necessary. The alignment of the absorber is measured along its full length so that sagging of the absorber can be quantified with this technique. The resulting absorber alignment measurement provides critical information required to accurately determine the intercept factor of a collector.

  11. GHOSTM: a GPU-accelerated homology search tool for metagenomics.

    Directory of Open Access Journals (Sweden)

    Shuji Suzuki

    Full Text Available BACKGROUND: A large number of sensitive homology searches are required for mapping DNA sequence fragments to known protein sequences in public and private databases during metagenomic analysis. BLAST is currently used for this purpose, but its calculation speed is insufficient, especially for analyzing the large quantities of sequence data obtained from a next-generation sequencer. However, faster search tools, such as BLAT, do not have sufficient search sensitivity for metagenomic analysis. Thus, a sensitive and efficient homology search tool is in high demand for this type of analysis. METHODOLOGY/PRINCIPAL FINDINGS: We developed a new, highly efficient homology search algorithm suitable for graphics processing unit (GPU calculations that was implemented as a GPU system that we called GHOSTM. The system first searches for candidate alignment positions for a sequence from the database using pre-calculated indexes and then calculates local alignments around the candidate positions before calculating alignment scores. We implemented both of these processes on GPUs. The system achieved calculation speeds that were 130 and 407 times faster than BLAST with 1 GPU and 4 GPUs, respectively. The system also showed higher search sensitivity and had a calculation speed that was 4 and 15 times faster than BLAT with 1 GPU and 4 GPUs. CONCLUSIONS: We developed a GPU-optimized algorithm to perform sensitive sequence homology searches and implemented the system as GHOSTM. Currently, sequencing technology continues to improve, and sequencers are increasingly producing larger and larger quantities of data. This explosion of sequence data makes computational analysis with contemporary tools more difficult. We developed GHOSTM, which is a cost-efficient tool, and offer this tool as a potential solution to this problem.

  12. IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments

    OpenAIRE

    Muhammad Tariq Pervez; Masroor Ellahi Babar; Asif Nadeem; Naeem Aslam; Nasir Naveed; Sarfraz Ahmad; Shah Muhammad; Salman Qadri; Muhammad Shahid; Tanveer Hussain; Maryam Javed

    2015-01-01

    IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reco...

  13. Custom Search Engines: Tools & Tips

    Science.gov (United States)

    Notess, Greg R.

    2008-01-01

    Few have the resources to build a Google or Yahoo! from scratch. Yet anyone can build a search engine based on a subset of the large search engines' databases. Use Google Custom Search Engine or Yahoo! Search Builder or any of the other similar programs to create a vertical search engine targeting sites of interest to users. The basic steps to…

  14. IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments.

    Science.gov (United States)

    Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Naeem; Naveed, Nasir; Ahmad, Sarfraz; Muhammad, Shah; Qadri, Salman; Shahid, Muhammad; Hussain, Tanveer; Javed, Maryam

    2015-01-01

    IVisTMSA is a software package of seven graphical tools for multiple sequence alignments. MSApad is an editing and analysis tool. It can load 409% more data than Jalview, STRAP, CINEMA, and Base-by-Base. MSA comparator allows the user to visualize consistent and inconsistent regions of reference and test alignments of more than 21-MB size in less than 12 seconds. MSA comparator is 5,200% efficient and more than 40% efficient as compared to BALiBASE c program and FastSP, respectively. MSA reconstruction tool provides graphical user interfaces for four popular aligners and allows the user to load several sequence files at a time. FASTA generator converts seven formats of alignments of unlimited size into FASTA format in a few seconds. MSA ID calculator calculates identity matrix of more than 11,000 sequences with a sequence length of 2,696 base pairs in less than 100 seconds. Tree and Distance Matrix calculation tools generate phylogenetic tree and distance matrix, respectively, using neighbor joining% identity and BLOSUM 62 matrix. PMID:25861209

  15. LASAGNA-Search: an integrated web tool for transcription factor binding site search and visualization.

    Science.gov (United States)

    Lee, Chic; Huang, Chun-Hsi

    2013-03-01

    The release of ChIP-seq data from the ENCyclopedia Of DNA Elements (ENCODE) and Model Organism ENCyclopedia Of DNA Elements (modENCODE) projects has significantly increased the amount of transcription factor (TF) binding affinity information available to researchers. However, scientists still routinely use TF binding site (TFBS) search tools to scan unannotated sequences for TFBSs, particularly when searching for lesser-known TFs or TFs in organisms for which ChIP-seq data are unavailable. The sequence analysis often involves multiple steps such as TF model collection, promoter sequence retrieval, and visualization; thus, several different tools are required. We have developed a novel integrated web tool named LASAGNA-Search that allows users to perform TFBS searches without leaving the web site. LASAGNA-Search uses the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm for TFBS alignment. Important features of LASAGNA-Search include (i) acceptance of unaligned variable-length TFBSs, (ii) a collection of 1726 TF models, (iii) automatic promoter sequence retrieval, (iv) visualization in the UCSC Genome Browser, and (v) gene regulatory network inference and visualization based on binding specificities. LASAGNA-Search is freely available at http://biogrid.engr.uconn.edu/lasagna_search/. PMID:23599922

  16. BFAST: an alignment tool for large scale genome resequencing.

    Directory of Open Access Journals (Sweden)

    Nils Homer

    Full Text Available BACKGROUND: The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation. METHODOLOGY: We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels. CONCLUSIONS: We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net.

  17. Protalign: a 3-dimensional protein alignment assessment tool.

    Science.gov (United States)

    Meads, D; Hansen, M D; Pang, A

    1999-01-01

    Protein fold recognition (sometimes called threading) is the prediction of a protein's 3-dimensional shape based on its similarity to a protein of known structure. Fold predictions are low resolution; that is, no effort is made to rotate the protein's component amino acid side chains into their correct spatial orientations. The goal is simply to recognize the protein family member that most closely resembles the target sequence of unknown structure and to create a sensible alignment of the target to the known structure (i.e., a structure-sequence alignment). To facilitate this type of structure prediction, we have designed a low resolution molecular graphics tool. ProtAlign introduces the ability to interact with and edit alignments directly in the 3-dimensional structure as well as in the usual 2-dimensional layout. It also contains several functions and features to help the user assess areas within the alignment. ProtAlign implements an open pipe architecture to allow other programs to access its molecular graphics capabilities. In addition, it is capable of "driving" other programs. Because amino acid side chain orientation is not relevant in fold recognition, we represent amino acid residues as abstract shapes or glyphs much like Lego (tm) blocks and we borrow techniques from comparative flow visualization using streamlines to provide clean depictions of the entire protein model. By creating a low resolution representation of protein structure, we are able to at least double the amount of information on the screen. At the same time, we create a view that is not as busy as the corresponding representations using traditional high resolution visualization methods which show detailed atomic structure. This eliminates distracting and possibly misleading visual clutter resulting from the mapping of protein alignment information onto a high resolution display of the known structure. This molecular graphics program is implemented in Open GL to facilitate porting to

  18. CATCHprofiles: Clustering and Alignment Tool for ChIP Profiles

    DEFF Research Database (Denmark)

    G. G. Nielsen, Fiona; Galschiøt Markus, Kasper; Møllegaard Friborg, Rune;

    2012-01-01

    Chromatin Immuno Precipitation (ChIP) profiling detects in vivo protein-DNA binding, and has revealed a large combinatorial complexity in the binding of chromatin associated proteins and their post-translational modifications. To fully explore the spatial and combinatorial patterns in ChIP-profil......Chromatin Immuno Precipitation (ChIP) profiling detects in vivo protein-DNA binding, and has revealed a large combinatorial complexity in the binding of chromatin associated proteins and their post-translational modifications. To fully explore the spatial and combinatorial patterns in Ch......IP-profiling data and detect potentially meaningful patterns, the areas of enrichment must be aligned and clustered, which is an algorithmically and computationally challenging task. We have developed CATCHprofiles, a novel tool for exhaustive pattern detection in ChIP profiling data. CATCHprofiles is built upon...... a computationally efficient implementation for the exhaustive alignment and hierarchical clustering of ChIP profiling data. The tool features a graphical interface for examination and browsing of the clustering results. CATCHprofiles requires no prior knowledge about functional sites, detects known binding patterns...

  19. MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data

    OpenAIRE

    Zhu, Zhengwei; Niu, Beifang; Chen, Jing; Wu, Sitao; Sun, Shulei; Li, Weizhong

    2012-01-01

    Summary: Numerous metagenomics projects have produced tremendous amounts of sequencing data. Aligning these sequences to reference genomes is an essential analysis in metagenomics studies. Large-scale alignment data call for intuitive and efficient visualization tool. However, current tools such as various genome browsers are highly specialized to handle intraspecies mapping results. They are not suitable for alignment data in metagenomics, which are often interspecies alignments. We have dev...

  20. Darwin on the Web: The Evolution of Search Tools.

    Science.gov (United States)

    Vidmar, Dale J.

    1999-01-01

    Discusses various search strategies and tools that can be used for searching on the Internet, including search engines and search directories; Boolean searching; metasearching; relevancy ranking; automatic phrase detection; backlinks; natural-language searching; clustering and cataloging information; image searching; customization and portals;…

  1. Missing Links: The Quest for Better Search Tools.

    Science.gov (United States)

    Kline, Vickie

    2002-01-01

    Examines a selection of innovative search tools that attempt to solve specific problems in searching. Topics include search difficulties, including controlled vocabularies and keyword searching; retrieval issues, including relevancy ranking; document discrimination problems; creating search tools for specific audiences; and interface design,…

  2. SOAP2: an improved ultrafast tool for short read alignment

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Yu, Chang; Li, Yingrui;

    2009-01-01

    SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for in...

  3. Strategic alignment: a performance tool (an empirical study of SMEs)

    OpenAIRE

    Jouirou, Nihel; Kalika, Michel

    2004-01-01

    The purpose of this research is to investigate whether the alignment of IT with the strategy (particularly the partnership strategy or cooperation practice) and organizational structure of an SME could have a decisive influence on its performance. We constructed a model and tested it empirically using data from 381 SMEs operating in different sectors. A multivariate perspective, modelled with structural equations, was used to test the alignment between strategy, structure and IT. The alignmen...

  4. GATA: A graphic alignment tool for comparative sequenceanalysis

    Energy Technology Data Exchange (ETDEWEB)

    Nix, David A.; Eisen, Michael B.

    2005-01-01

    Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dotplot analysis is often used to estimate non-coding sequence relatedness. Yet dot plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.

  5. GATA: a graphic alignment tool for comparative sequence analysis

    OpenAIRE

    Nix David A; Eisen Michael B

    2005-01-01

    Abstract Background Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collineari...

  6. A tabu search algorithm for post-processing multiple sequence alignment.

    Science.gov (United States)

    Riaz, Tariq; Yi, Wang; Li, Kuo-Bin

    2005-02-01

    Tabu search is a meta-heuristic approach that is proven to be useful in solving combinatorial optimization problems. We implement the adaptive memory features of tabu search to refine a multiple sequence alignment. Adaptive memory helps the search process to avoid local optima and explores the solution space economically and effectively without getting trapped into cycles. The algorithm is further enhanced by introducing extended tabu search features such as intensification and diversification. The neighborhoods of a solution are generated stochastically and a consistency-based objective function is employed to measure its quality. The algorithm is tested with the datasets from BAliBASE benchmarking database. We have observed through experiments that tabu search is able to improve the quality of multiple alignments generated by other software such as ClustalW and T-Coffee. The source code of our algorithm is available at http://www.bii.a-star.edu.sg/~tariq/tabu/. PMID:15751117

  7. Local Alignment Tool Based on Hadoop Framework and GPU Architecture

    OpenAIRE

    2014-01-01

    With the rapid growth of next generation sequencing technologies, such as Slex, more and more data have been discovered and published. To analyze such huge data the computational performance is an important issue. Recently, many tools, such as SOAP, have been implemented on Hadoop and GPU parallel computing architectures. BLASTP is an important tool, implemented on GPU architectures, for biologists to compare protein sequences. To deal with the big biology data, it is hard to rely on single G...

  8. Evaluating semantic search tools using the SEALS platform

    OpenAIRE

    Wrigley, S.N.; Elbedweihy, K; Reinhardt, D.; Bernstein, A; Ciravegna, F.

    2010-01-01

    In common with many state of the art semantic technologies, there is a lack of comprehensive, established evaluation mechanisms for semantic search tools. In this paper, we describe a new evaluation and benchmarking approach for semantic search tools using the infrastructure under development within the SEALS initiative. To our knowledge, it is the first effort to present a comprehensive evaluation methodology for semantic search tools. The paper describes the evaluation methodology including...

  9. Local Alignment Tool Based on Hadoop Framework and GPU Architecture

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2014-01-01

    Full Text Available With the rapid growth of next generation sequencing technologies, such as Slex, more and more data have been discovered and published. To analyze such huge data the computational performance is an important issue. Recently, many tools, such as SOAP, have been implemented on Hadoop and GPU parallel computing architectures. BLASTP is an important tool, implemented on GPU architectures, for biologists to compare protein sequences. To deal with the big biology data, it is hard to rely on single GPU. Therefore, we implement a distributed BLASTP by combining Hadoop and multi-GPUs. The experimental results present that the proposed method can improve the performance of BLASTP on single GPU, and also it can achieve high availability and fault tolerance.

  10. Local alignment tool based on Hadoop framework and GPU architecture.

    Science.gov (United States)

    Hung, Che-Lun; Hua, Guan-Jie

    2014-01-01

    With the rapid growth of next generation sequencing technologies, such as Slex, more and more data have been discovered and published. To analyze such huge data the computational performance is an important issue. Recently, many tools, such as SOAP, have been implemented on Hadoop and GPU parallel computing architectures. BLASTP is an important tool, implemented on GPU architectures, for biologists to compare protein sequences. To deal with the big biology data, it is hard to rely on single GPU. Therefore, we implement a distributed BLASTP by combining Hadoop and multi-GPUs. The experimental results present that the proposed method can improve the performance of BLASTP on single GPU, and also it can achieve high availability and fault tolerance. PMID:24955362

  11. THoR: a tool for domain discovery and curation of multiple alignments

    OpenAIRE

    Dickens, N.J.; Ponting, C. P.

    2003-01-01

    We describe a tool, THoR, that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an accurate and comprehensive alignment for any domain family. The entire process is designed for use via a web-browser, with simple links and cross-references to relevant information, to assist the assessment of biological significance. THoR has been benchmarked for accuracy using the SMART and pufferfish ge...

  12. PFAAT version 2.0 : A tool for editing, annotating, and analyzing multiple sequence alignments

    OpenAIRE

    Somaroo Shyamal; Wang Yaoyu E; Hong Eun-Jong; Ocano Marco; Mathur Vidhya; Dana Paul H; Caffrey Daniel R; Caffrey Brian E; Potluri Shobha; Huang Enoch S

    2007-01-01

    Abstract Background By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. Results Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple a...

  13. MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lamarche, Brian L.; Crowell, Kevin L.; Jaitly, Navdeep; Petyuk, Vladislav A.; Shah, Anuj R.; Polpitiya, Ashoka D.; Sandoval, John D.; Kiebel, Gary R.; Monroe, Matthew E.; Callister, Stephen J.; Metz, Thomas O.; Anderson, Gordon A.; Smith, Richard D.

    2013-02-12

    MultiAlign is a free software tool that aligns multiple liquid chromatography-mass spectrometry datasets to one another by clustering mass and LC elution features across datasets. Applicable to both label-free proteomics and metabolomics comparative analyses, the software can be operated in several modes. Clustered features can be matched to a reference database to identify analytes, used to generate abundance profiles, linked to tandem mass spectra based on parent precursor masses, and culled for targeted liquid chromatography-tandem mass spectrometric analysis. MultiAlign is also capable of tandem mass spectral clustering to describe proteome structure and find similarity in subsequent sample runs.

  14. Challenging Google, Microsoft Unveils a Search Tool for Scholarly Articles

    Science.gov (United States)

    Carlson, Scott

    2006-01-01

    Microsoft has introduced a new search tool to help people find scholarly articles online. The service, which includes journal articles from prominent academic societies and publishers, puts Microsoft in direct competition with Google Scholar. The new free search tool, which should work on most Web browsers, is called Windows Live Academic Search…

  15. Summary Report for the SINBAD Search Tool Project

    Energy Technology Data Exchange (ETDEWEB)

    Cunha Da Silva, Alice [ORNL

    2012-06-01

    The Shielding Integral Benchmark Archive Database (SINBAD) Search Tool has been developed to serve as an interface with the SINBAD database to facilitate a simple and quick means of searching for information related to experimental benchmark problems. The Search Tool is written in Java and provides a better and efficient way to retrieve information from the SINBAD database. Searches can be performed quickly and easily. With regard to improvements, users are no longer required to know the name of the benchmarks to search the database. Instead, a search can be performed by specifying the experimental facility, constituents of the experimental benchmark, etc. In summary, a new powerful database search tool has been developed for SINBAD.

  16. Developing a Grid-Based Search and Categorization Tool

    OpenAIRE

    Haya, Glenn; Scholze, Frank; Vigen, Jens

    2003-01-01

    Grid technology has the potential to improve the accessibility of digital libraries. The participants in Project GRACE (Grid Search And Categorization Engine) are in the process of developing a search engine that will allow users to search through heterogeneous resources stored in geographically distributed digital collections. What differentiates this project from current search tools is that GRACE will be run on the European Data Grid, a large distributed network, and will not have a single...

  17. ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output.

    Science.gov (United States)

    Zaal, Dionne; Nota, Benjamin

    2016-01-01

    We present ADOMA, a command line tool that produces alternative outputs from ClustalW multiple alignments of nucleotide or protein sequences. ADOMA can simplify the output of alignments by showing only the different residues between sequences, which is often desirable when only small differences such as single nucleotide polymorphisms are present (e.g., between different alleles). Another feature of ADOMA is that it can enhance the ClustalW output by coloring the residues in the alignment. This tool is easily integrated into automated Linux pipelines for next-generation sequencing data analysis, and may be useful for researchers in a broad range of scientific disciplines including evolutionary biology and biomedical sciences. The source code is freely available at https://sourceforge. net/projects/adoma/. PMID:27491653

  18. Surveying and optical tooling technologies combined to align a skewed beamline at the LAMPF accelerator

    International Nuclear Information System (INIS)

    Optical Tooling evolved from traditional surveying, and both technologies are sometimes used interchangeably in large industrial installations, since the instruments and their specialized adapters and supports complement each other well. A unique marriage of both technologies was accomplished in a novel application at LAMPF, the Los Alamos Meson Physics Facility. LAMPF consists of a linear accelerator with multiple target systems, one of which had to be altered to accommodate a new beamline for a neutrino experiment. The new line was to be installed into a crowded beam tunnel and had to be skewed and tilted in compound angles to avoid existing equipment. In this paper we describe how Optical Tooling was used in conjunction with simple alignment and reference fixtures to set fiducials on the magnets and other mechanical components of the beamline, and how theodolites and sight levels were then adapted to align these components along the calculated skew planes. Design tolerances are compared with measured alignment results

  19. Mathematics and Logic as Information Compression by Multiple Alignment, Unification and Search

    OpenAIRE

    Wolff, J Gerard

    2003-01-01

    This article introduces the conjecture that "mathematics, logic and related disciplines may usefully be understood as information compression (IC) by 'multiple alignment', 'unification' and 'search' (ICMAUS)". As a preparation for the two main sections of the article, concepts of information and information compression are reviewed. Related areas of research are also described including IC in brains and nervous systems, and IC in relation to inductive inference, Minimum Length Encoding and pr...

  20. AMAS: a fast tool for alignment manipulation and computing of summary statistics.

    Science.gov (United States)

    Borowiec, Marek L

    2016-01-01

    The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package. AMAS works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. The manipulation functions include conversions among popular formats, concatenation, extracting sites and splitting according to a pre-defined partitioning scheme, creation of replicate data sets, and removal of taxa. The statistics calculated include the number of taxa, alignment length, total count of matrix cells, overall number of undetermined characters, percent of missing data, AT and GC contents (for DNA alignments), count and proportion of variable sites, count and proportion of parsimony informative sites, and counts of all characters relevant for a nucleotide or amino acid alphabet. AMAS is particularly suitable for very large alignments with hundreds of taxa and thousands of loci. It is computationally efficient, utilizes parallel processing, and performs better at concatenation than other popular tools. AMAS is a Python 3 program that relies solely on Python's core modules and needs no additional dependencies. AMAS source code and manual can be downloaded from http://github.com/marekborowiec/AMAS/ under GNU General Public License. PMID:26835189

  1. The Interestingness Tool for Search in the Web

    OpenAIRE

    Exman, Iaakov; Amar, Gilad; Shaltiel, Ran

    2014-01-01

    Interestingness,as the composition of Relevance and Unexpectedness, has been tested by means of Web search cases studies and led to promising results. But for thorough investigation and routine practical application one needs a flexible and robust tool. This work describes such an Interestingness based search tool, its software architecture and actual implementation. One of its flexibility traits is the choice of Interestingness functions: it may work with Match-Mismatch and Tf-Idf, among oth...

  2. GraphCrunch 2: Software tool for network modeling, alignment and clustering

    Directory of Open Access Journals (Sweden)

    Hayes Wayne

    2011-01-01

    Full Text Available Abstract Background Recent advancements in experimental biotechnology have produced large amounts of protein-protein interaction (PPI data. The topology of PPI networks is believed to have a strong link to their function. Hence, the abundance of PPI data for many organisms stimulates the development of computational techniques for the modeling, comparison, alignment, and clustering of networks. In addition, finding representative models for PPI networks will improve our understanding of the cell just as a model of gravity has helped us understand planetary motion. To decide if a model is representative, we need quantitative comparisons of model networks to real ones. However, exact network comparison is computationally intractable and therefore several heuristics have been used instead. Some of these heuristics are easily computable "network properties," such as the degree distribution, or the clustering coefficient. An important special case of network comparison is the network alignment problem. Analogous to sequence alignment, this problem asks to find the "best" mapping between regions in two networks. It is expected that network alignment might have as strong an impact on our understanding of biology as sequence alignment has had. Topology-based clustering of nodes in PPI networks is another example of an important network analysis problem that can uncover relationships between interaction patterns and phenotype. Results We introduce the GraphCrunch 2 software tool, which addresses these problems. It is a significant extension of GraphCrunch which implements the most popular random network models and compares them with the data networks with respect to many network properties. Also, GraphCrunch 2 implements the GRAph ALigner algorithm ("GRAAL" for purely topological network alignment. GRAAL can align any pair of networks and exposes large, dense, contiguous regions of topological and functional similarities far larger than any other

  3. Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST

    Directory of Open Access Journals (Sweden)

    Oliver Melvin J

    2005-04-01

    Full Text Available Abstract Background BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST, which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. Results W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN. W.ND-BLAST provides intuitive Graphic User Interfaces (GUI for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. Conclusion W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is

  4. Phylo-VISTA: An interactive visualization tool for multiple DNAsequence alignments

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Nameeta; Couronne, Olivier; Pennacchio, Len A.; Brudno,Michael; Batzoglou, Serafim; Bethel, E. Wes; Rubin, Edward M.; Hamann,Bernd; Dubchak, Inna

    2003-04-25

    Motivation. The power of multi-sequence comparison forbiological discovery is well established and sequence data from a growinglist of organisms is becoming available. Thus, a need exists forcomputational strategies to visually compare multiple aligned sequencesto support conservation analysis across various species. To be efficientthese visualization algorithms require the ability to universally handlea wide range of evolutionary distances while taking into accountphylogeny Results. We have developed Phylo-VISTA, an interactive tool foranalyzing multiple alignments by visualizing the similarity of DNAsequences among multiple species while considering their phylogenicrelationships. Features include a broad spectrum of resolution parametersfor examining the alignment and the ability to easily compare any subtreeof sequences within a complete alignment dataset. Phylo-VISTA uses VISTAconcepts that have been successfully applied previously to a wide rangeof comparative genomics data analysis problems. Availability Phylo-VISTAis an interactive java applet available for downloading athttp://graphics.cs.ucdavis.edu/~;nyshah/Phylo-VISTA. It is also availableon-line at http://www-gsd.lbl.gov/phylovista and is integrated with theglobal alignment program LAGAN athttp://lagan.stanford.edu.Contactphylovista@lbl.gov

  5. iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2.

    Science.gov (United States)

    Yang, Chung-Han; Shih, Cheng-Ting; Chen, Kun-Tze; Lee, Po-Han; Tsai, Ping-Han; Lin, Jian-Cheng; Yen, Ching-Yu; Lin, Tiao-Yin; Lu, Chin Lung

    2016-07-01

    Since its first release in 2010, iPARTS has become a valuable tool for globally or locally aligning two RNA 3D structures. It was implemented by a structural alphabet (SA)-based approach, which uses an SA of 23 letters to reduce RNA 3D structures into 1D sequences of SA letters and applies traditional sequence alignment to these SA-encoded sequences for determining their global or local similarity. In this version, we have re-implemented iPARTS into a new web server iPARTS2 by constructing a totally new SA, which consists of 92 elements with each carrying both information of base and backbone geometry for a representative nucleotide. This SA is significantly different from the one used in iPARTS, because the latter consists of only 23 elements with each carrying only the backbone geometry information of a representative nucleotide. Our experimental results have shown that iPARTS2 outperforms its previous version iPARTS and also achieves better accuracy than other popular tools, such as SARA, SETTER and RASS, in RNA alignment quality and function prediction. iPARTS2 takes as input two RNA 3D structures in the PDB format and outputs their global or local alignments with graphical display. iPARTS2 is now available online at http://genome.cs.nthu.edu.tw/iPARTS2/. PMID:27185896

  6. An overview of steps and tools for the corporate real estate strategy alignment process

    OpenAIRE

    2014-01-01

    Purpose – Strategic thinking is a continuous process, alternating between thinking, planning and evaluating. Corporate Real Estate Management (CREM) needs to align their strategy and activities to corporate strategy during this entire process that the organisation goes through. Along the way, many different issues need to be considered and tools used to help make the right decisions. This paper aims to provide an overview of the strategic thinking process, and identify important steps to take...

  7. Simrank: Rapid and sensitive general-purpose k-mer search tool

    Energy Technology Data Exchange (ETDEWEB)

    DeSantis, T.Z.; Keller, K.; Karaoz, U.; Alekseyenko, A.V; Singh, N.N.S.; Brodie, E.L; Pei, Z.; Andersen, G.L; Larsen, N.

    2011-04-01

    Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project (http://nihroadmap.nih.gov/hmp). Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.

  8. Developing a Grid-based search and categorization tool

    CERN Document Server

    Haya, Glenn; Vigen, Jens

    2003-01-01

    Grid technology has the potential to improve the accessibility of digital libraries. The participants in Project GRACE (Grid Search And Categorization Engine) are in the process of developing a search engine that will allow users to search through heterogeneous resources stored in geographically distributed digital collections. What differentiates this project from current search tools is that GRACE will be run on the European Data Grid, a large distributed network, and will not have a single centralized index as current web search engines do. In some cases, the distributed approach offers advantages over the centralized approach since it is more scalable, can be used on otherwise inaccessible material, and can provide advanced search options customized for each data source.

  9. Improving the performance of the actinic inspection tool with an optimized alignment procedure

    International Nuclear Information System (INIS)

    Extreme ultraviolet (EUV) microscopy is an important tool for the investigation of the performance of EUV masks, for detecting the presence and the characteristics of defects, and for evaluating the effectiveness of defect repair techniques. Aerial image measurement bypasses the difficulties inherent to photoresist imaging and enables high data collection speed and flexibility. It provides reliable and quick feedback for the development of masks and lithography system modeling methods. We operate the SEMATECH Berkeley Actinic Inspection Tool (AIT), a EUV microscope installed at the Advanced Light Source at Lawrence Berkeley National Laboratory. The AIT is equipped with several high-magnification Fresnel zoneplate lenses, with various numerical aperture values, that enable it image the reflective mask surface with various resolution and magnification settings. Although the AIT has undergone significant recent improvements in terms of imaging resolution and illumination uniformity, there is still room for improvement. In the AIT, an off-axis zoneplate lens collects the light coming from the sample and an image of the sample is projected onto an EUV-sensitive CCD camera. The simplicity of the optical system is particularly helpful considering that the AIT alignment has to be performed every time that a sample or a zoneplate is replaced. The alignment is sensitive to several parameters such as the lens position and orientation, the illumination direction and the sample characteristics. Since the AIT works in high vacuum, there is no direct access to the optics or to the sample during the alignment and the measurements. For all these reasons the alignment procedures and feedback can be complex, and in some cases can reduce the overall data throughput of the system. In this paper we review the main strategies and procedures that have been developed for quick and reliable alignments, and we describe the performance improvements we have achieved, in terms of aberration

  10. Improving the performance of the actinic inspection tool with an optimized alignment procedure

    Energy Technology Data Exchange (ETDEWEB)

    Mochi, I.; Goldberg, K.A.; Naulleau, P.; Huh, Sungmin

    2009-03-04

    Extreme ultraviolet (EUV) microscopy is an important tool for the investigation of the performance of EUV masks, for detecting the presence and the characteristics of defects, and for evaluating the effectiveness of defect repair techniques. Aerial image measurement bypasses the difficulties inherent to photoresist imaging and enables high data collection speed and flexibility. It provides reliable and quick feedback for the development of masks and lithography system modeling methods. We operate the SEMATECH Berkeley Actinic Inspection Tool (AIT), a EUV microscope installed at the Advanced Light Source at Lawrence Berkeley National Laboratory. The AIT is equipped with several high-magnification Fresnel zoneplate lenses, with various numerical aperture values, that enable it image the reflective mask surface with various resolution and magnification settings. Although the AIT has undergone significant recent improvements in terms of imaging resolution and illumination uniformity, there is still room for improvement. In the AIT, an off-axis zoneplate lens collects the light coming from the sample and an image of the sample is projected onto an EUV-sensitive CCD camera. The simplicity of the optical system is particularly helpful considering that the AIT alignment has to be performed every time that a sample or a zoneplate is replaced. The alignment is sensitive to several parameters such as the lens position and orientation, the illumination direction and the sample characteristics. Since the AIT works in high vacuum, there is no direct access to the optics or to the sample during the alignment and the measurements. For all these reasons the alignment procedures and feedback can be complex, and in some cases can reduce the overall data throughput of the system. In this paper we review the main strategies and procedures that have been developed for quick and reliable alignments, and we describe the performance improvements we have achieved, in terms of aberration

  11. DETERMINATION OF BALL COHESIVE AND FRICTIONAL FORCES WITH TOOL AT POLISHING BETWEEN ALIGNED RINGS AND DISK

    Directory of Open Access Journals (Sweden)

    K. G. Schetnikovich

    2010-01-01

    Full Text Available The paper provides a design description of a tool used for polishing balls made of brittle materials between bottom driving disk and two rings. An external stationary ring has a ring turning of rectangular profile that helps the ring to be based directly on the balls which are to be polished and take self-aligned position in relation to tool rotation axis.  Forces acting on the balls in the points of contact with the tool with due account of friction against a separator and conditions of ball sliding along ring working surfaces are determined in the paper. Dependence for determination of stationary and driving ring load ratio when balls are sliding along two contact surfaces of the tool is ascertained in the paper. The paper contains recommendations on selection of modes for ball polishing at its initial and finishing stages.

  12. Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

    OpenAIRE

    Lee DT; Shih Arthur; Peng Chin-Lin; Wu Yu-Wei

    2007-01-01

    Abstract Background When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the ali...

  13. STAR3D: a stack-based RNA 3D structural alignment tool.

    Science.gov (United States)

    Ge, Ping; Zhang, Shaojie

    2015-11-16

    The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time. PMID:26184875

  14. Alignment tools used to locate a wire and a laser beam in the VISA undulator project

    International Nuclear Information System (INIS)

    Within the framework of the LCLS (Linac Coherent Light Source), a small experiment VISA (Visual to Infrared SASE (Self Amplified Stimulated Emission) Amplifier) is being performed at Brookhaven National Laboratory. VISA consists of four wiggler segments, each 0.99 m long. The four segments are required to be aligned to the beam axis with an rms error less than 50 μm. This very demanding alignment is carried out in two steps. First the segments are fiducialized using a pulsed wire system. Then the wiggler segments are placed along a reference laser beam which coincides with the electron beam axis. In the wiggler segment fiducialization, a wire is stretched through a wiggler segment and a current pulse is sent down the wire. The deflection of the wire is monitored. The deflection gives information about the electron beam trajectory. The wire is moved until its x position, the coordinate without wire sag, is on the ideal beam trajectory. (The y position is obtained by rotating the wiggler 90 deg C.) Once the wire is on the ideal beam trajectory, the wire's location is measured relative to tooling balls on the wiggler segment. To locate the wire, a device was constructed which measures the wire position relative to tooling balls on the device. The device is called the wire finder. It will be discussed in this paper. To place the magnets along the reference laser beam, the position of the laser beam must be determined. A device which can locate the laser beam relative to tooling balls was constructed and is also discussed in this paper. This device is called the laser finder. With a total alignment error budget less than 50 μm, both the fiducialization and magnet placement must be performed with errors much smaller than 50 μm. It is desired to keep the errors from the wire finder and laser finder at the few μm level. (authors)

  15. Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

    Directory of Open Access Journals (Sweden)

    Lee DT

    2007-02-01

    Full Text Available Abstract Background When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences. Results A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. Conclusion With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL http://biocomp.iis.sinica.edu.tw/phylomlogo.

  16. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

    OpenAIRE

    Zhao, Yongan; Tang, Haixu; Ye, Yuzhen

    2011-01-01

    Summary: With the wide application of next-generation sequencing (NGS) techniques, fast tools for protein similarity search that scale well to large query datasets and large databases are highly desirable. In a previous work, we developed RAPSearch, an algorithm that achieved a ~20–90-fold speedup relative to BLAST while still achieving similar levels of sensitivity for short protein fragments derived from NGS data. RAPSearch, however, requires a substantial memory footprint to identify align...

  17. ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search

    OpenAIRE

    Ge, Ping; Zhong, Cuncong; Zhang, Shaojie

    2014-01-01

    Background Recent advances in RNA structure probing technologies, including the ones based on high-throughput sequencing, have improved the accuracy of thermodynamic folding with quantitative nucleotide-resolution structural information. Results In this paper, we present a novel approach, ProbeAlign, to incorporate the reactivities from high-throughput RNA structure probing into ncRNA homology search for functional annotation. To reduce the overhead of structure alignment on large-scale data,...

  18. 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.

  19. Tools for Search, Analysis and Management of Patent Portfolios

    Directory of Open Access Journals (Sweden)

    Muqbil Burhan,

    2012-05-01

    Full Text Available Patents have been acknowledged worldwide as rich sources of information for technology forecasting,competitive analysis and management of patent portfolios. Because of the high potential of patents as animportant indicator of various technology measurements and as econometric measure, patent analysis hasbecome vital for corporate world and of interest to academic research. Retrieving relevant prior art, concerningthe technology of interest, has been vital for managers and consultants dealing with intellectual propertyrights. Tremendous progress in the field of electronic search tools as of late has led to a specialised and lesstime consuming search capabilities even in the fields where search is mostly based on formulas, drawingsand flowcharts. Online patent databases and various other analytical tools have given patent analysis animportant edge, which otherwise required extensive and time consuming data collection and calculations.Patents provide valuable information which could be used for various purposes by industry, academia, andpolicy analysts. This article explores the various options and tools available for patent search, analysis andmanagement of patent portfolios, for efficiently identifying the relevant prior art, managing their own patentclusters and/or competitive intelligence.

  20. Simple scalable nucleotic FPGA based short read aligner for exhaustive search of substitution errors

    Directory of Open Access Journals (Sweden)

    Fehér Péter

    2015-12-01

    Full Text Available With the advent of the new and continuously improving technologies, in a couple of years DNA sequencing can be as commonplace as a simple blood test. The growth of sequencing efficiency has a larger exponent than the Moore’s law of standard processors, hence alignment and further processing of sequenced data is the bottleneck. The usage of FPGA (Field Programmable Gate Arrays technology may provide an efficient alternative. We propose a simple algorithm for DNA sequence alignment, which can be realized efficiently by nucleotic principal agents of Non.Neumann nature. The prototype FPGA implementation runs on a small Terasic DE1-SoC demo board with a Cyclone V chip. We present test results and furthermore analyse the theoretical scalability of this system, showing that the execution time is independent of the length of reference genome sequences. A special advantage of this parallel algorithm is that it performs exhaustive search producing all match variants up to a predetermined number of point (mutation errors.

  1. Utilizing AFIS searching tools to reduce errors in fingerprint casework.

    Science.gov (United States)

    Langenburg, Glenn; Hall, Carey; Rosemarie, Quincy

    2015-12-01

    Fifty-six (56) adjudicated, property crime cases involving fingerprint evidence were reviewed using a case-specific AFIS database tool. This tool allowed fingerprint experts to search latent prints in the cases against a database of friction ridge exemplars limited to only the individuals specific to that particular case. We utilized three different methods to encode and search the latent prints: automatic feature extraction, manual encoding performed by a student intern, and manual encoding performed by a fingerprint expert. Performance in the study was strongest when the encoding was conducted by the fingerprint expert. The results of the study showed that while the AFIS tools failed to locate all of the identifications originally reported by the initial fingerprint expert that worked the case, the AFIS tools helped to identify 7 additional latent prints that were not reported by the initial fingerprint expert. We conclude that this technology, when combined with fingerprint expertise, will reduce the number of instances where an erroneous exclusion could occur, increase the efficiency of a fingerprint unit, and be a useful tool for reviewing active or cold cases for missed opportunities to report identifications. PMID:26295930

  2. Optimizing GoTools' Search Heuristics using Genetic Algorithms

    OpenAIRE

    Pratola, Matthew; Wolf, Thomas

    2003-01-01

    GoTools is a program which solves life & death problems in the game of Go. This paper describes experiments using a Genetic Algorithm to optimize heuristic weights used by GoTools' tree-search. The complete set of heuristic weights is composed of different subgroups, each of which can be optimized with a suitable fitness function. As a useful side product, an MPI interface for FreePascal was implemented to allow the use of a parallelized fitness function running on a Beowulf cluster. The aim ...

  3. GOKaRT: Graphical Online Search Tool for Maps

    Directory of Open Access Journals (Sweden)

    Mechthild Schüler

    2008-09-01

    Full Text Available The map department of the Staats- und Universitätsbibliothek Göttingen together with the Berlin State Library propose a project to develop a web-based graphic cataloguing and search system for maps, to be funded by the German Research Foundation. This tool shall be made available to all map holdings in archives, libraries, university departments and museums in Germany as a comfortable means for the administration of map holdings and as a search tool. Sheets belonging to map series as well as single maps (old and new will be registered cooperatively by the participants with simple tools. This cooperation in data maintenance will facilitate the work especially for understaffed map holdings. Depending on the type of map there are four different mechanisms for map reference. For map series electronic index sheets are used which will show information regarding the various issues of the map sheets. Due to the intuitive graphic search entry GOKaRT-users will easily find the required maps of a certain region available in a chosen holding. User administration modules ensure comfortable handling. GOKaRT is being developed on the basis of licence-free open source programmes. In case financing is provided by the German Research Foundation, GOKaRT can be used free of charge internationally. This would require a contract stipulating data exchange between the partners as well as permanent storage and usability of the data.

  4. zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles

    Energy Technology Data Exchange (ETDEWEB)

    Ovcharenko, I. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Energy, Environment and Institutional Computing; Genome Biology Division; Loots, G. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Genome Biology Division; Hardison, R. C. [Pennsylvania State Univ., Univ. Park, PA (United States). Dept. of Computer Science and Engineering; Miller., W. [Pennsylvania State Univ., Univ. Park, PA (United States). Dept. of Computer Science and Engineering; Dept. of Biology; Stubbs, L. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Genome Biology Division

    2004-03-01

    Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here we introduce zPicture (http://zpicture.dcode.org), an interactive web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionary conserved regions (ECRs). zPicture is highly flexible because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates. We demonstrate the application of this module to identify a known regulatory element in the HOXD locus, where functional ECRs are difficult to discern against the highly conserved genomic background. zPicture also facilitates transcription factor binding site analysis via the rVISTA tool portal. We present an example of the HBB complex when zPicture/rVista combination specifically pinpoints to two ECRs containing GATA- 1, NF-E2 and TAL1/E47 binding sites that were previously identified as transcriptional enhancers. In addition, zPicture is linked to the UCSC Genome Browser allowing users to automatically extract sequences and gene annotations for any recorded locus. Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes including those of microbial organisms.

  5. In search of a potential diagnostic tool for molecular characterization of lymphatic filariasis.

    Science.gov (United States)

    Saeed, Mohd; Adnan, Mohd; Khan, Saif; Al-Shammari, Eyad; Mustafa, Huma

    2016-01-01

    Lymphatic filariasis (LF) is a chronic disease and is caused by the parasites Wuchereria bancrofti (W. bancrofti), Brugia malayi (B. malayi) and Brugia timori (B. timori). In the present study, Setaria cervi (S. cervi), a bovine filarial parasite has been used. Previously, it has been reported that the S. cervi shares some common proteins and antigenic determinants with that of human filarial parasite. The larval stages of filarial species usually cannot be identified by classical morphology. Hence, molecular characterization allows the identification of the parasites throughout all their developmental stages. The genomic DNA of S. cervi adult were isolated and estimated spectrophotometrically for the quantitative presence of DNA content. Screening of DNA sequences from filarial DNA GenBank and Expressed Sequence Tags (EST's) were performed for homologous sequences and then multiple sequence alignment was executed. The conserved sequences from multiple sequence alignment were used for In Silico primer designing. The successfully designed primers were used further in PCR amplifications. Therefore, in search of a promising diagnostic tool few genes were identified to be conserved in the human and bovine filariasis and these novel primers deigned may help to develop a promising diagnostic tool for identification of lymphatic filariasis. PMID:26751881

  6. RAPSearch: a fast protein similarity search tool for short reads

    Directory of Open Access Journals (Sweden)

    Choi Jeong-Hyeon

    2011-05-01

    Full Text Available Abstract Background Next Generation Sequencing (NGS is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets. Results We developed a fast protein similarity search tool RAPSearch that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. For short reads (translated in 6 frames we tested, RAPSearch achieved ~20-90 times speedup as compared to BLASTX. RAPSearch missed only a small fraction (~1.3-3.2% of BLASTX similarity hits, but it also discovered additional homologous proteins (~0.3-2.1% that BLASTX missed. By contrast, BLAT, a tool that is even slightly faster than RAPSearch, had significant loss of sensitivity as compared to RAPSearch and BLAST. Conclusions RAPSearch is implemented as open-source software and is accessible at http://omics.informatics.indiana.edu/mg/RAPSearch. It enables faster protein similarity search. The application of RAPSearch in metageomics has also been demonstrated.

  7. BlastMultAl, a Blast Extension for Similarity Searching with Alignment Graphs

    OpenAIRE

    Nicodème, Pierre

    1996-01-01

    We describe a new method of processing similarity queries of a proteic multiple alignment with a set (database) of protein sequences, or similarity queries of a protein sequence with a set of protein alignments. We use a representation of multiple alignments as alignment-graphs. Comparisons with different classical methods is made. This new method allows the detection of subtle similarities which are not found by the other methods. It has direct applications for similarities querying with the...

  8. Search for Technihadrons in Dielectron channel and alignments of the ATLAS liquid Argon Electromagnetic calorimeters

    International Nuclear Information System (INIS)

    The LHC campaign in the first years of data taking was successful. The 2011 run has allowed to record more than 5 fb-1 of data at √(s) = 7 TeV with the ATLAS experiment. In the work presented in this this thesis the whole 2011 data set is used to performed different studies. This thesis is organized in five chapters. In the first chapter is presented a theoretical introduction to the Standard Model (SM) and to one of its possible extension the TechniColor model (TC). The second chapter gives an overview of the LHC complex and of the ATLAS detector components. In the third chapter the timing analysis on all the readout channels of the Liquid Argon Calorimeter is reported. A precise timing alignment over the whole calorimeter is used to synchronize the detector readout system with the LHC bunch crossing and has also application in some physics analysis such as those looking for long lived particles. In the searches for new phenomena an excellent electron identification capability, with high efficiency and high jet rejection rate, is required over a broad energy range. The fourth chapter of this thesis presents the measurements of the trigger and the identification electron efficiency using Z → ee events. Finally the last chapter describes a search for resonant deviations from the Standard Model in the high masses of the dielectron spectrum within two different Technicolor scenarios the Low-scale Technicolor and the Minimal Walking Technicolor. The significance of potential excess of the TC candidate events over the SM background expectation is evaluated in the dilepton invariant mass distribution. In the absence of any significant signal 95% confidence level limits are set on the cross section and on the resonance mass. (author)

  9. PHOG-BLAST – a new generation tool for fast similarity search of protein families

    Directory of Open Access Journals (Sweden)

    Mironov Andrey A

    2006-06-01

    Full Text Available Abstract Background The need to compare protein profiles frequently arises in various protein research areas: comparison of protein families, domain searches, resolution of orthology and paralogy. The existing fast algorithms can only compare a protein sequence with a protein sequence and a profile with a sequence. Algorithms to compare profiles use dynamic programming and complex scoring functions. Results We developed a new algorithm called PHOG-BLAST for fast similarity search of profiles. This algorithm uses profile discretization to convert a profile to a finite alphabet and utilizes hashing for fast search. To determine the optimal alphabet, we analyzed columns in reliable multiple alignments and obtained column clusters in the 20-dimensional profile space by applying a special clustering procedure. We show that the clustering procedure works best if its parameters are chosen so that 20 profile clusters are obtained which can be interpreted as ancestral amino acid residues. With these clusters, only less than 2% of columns in multiple alignments are out of clusters. We tested the performance of PHOG-BLAST vs. PSI-BLAST on three well-known databases of multiple alignments: COG, PFAM and BALIBASE. On the COG database both algorithms showed the same performance, on PFAM and BALIBASE PHOG-BLAST was much superior to PSI-BLAST. PHOG-BLAST required 10–20 times less computer memory and computation time than PSI-BLAST. Conclusion Since PHOG-BLAST can compare multiple alignments of protein families, it can be used in different areas of comparative proteomics and protein evolution. For example, PHOG-BLAST helped to build the PHOG database of phylogenetic orthologous groups. An essential step in building this database was comparing protein complements of different species and orthologous groups of different taxons on a personal computer in reasonable time. When it is applied to detect weak similarity between protein families, PHOG-BLAST is less

  10. Development of a helmet/helmet-display-unit alignment tool (HAT) for the Apache helmet and display unit

    Science.gov (United States)

    McLean, William; Statz, Jonathan; Estes, Victor; Booms, Shawn; Martin, John S.; Harding, Thomas

    2015-05-01

    Project Manager (PM) Apache Block III contacted the U.S. Army Aeromedical Research Laboratory (USAARL), Fort Rucker, Alabama, requesting assistance to evaluate and find solutions to a government-developed Helmet Display Unit (HDU) device called the Mock HDU for helmet alignment of the Apache Advanced Integrated Helmet (AAIH). The AAIH is a modified Head Gear Unit No. 56 for Personnel (HGU-56/P) to replace the current Integrated Helmet and Sighting System (IHADSS). The current flashlight-based HDU simulator for helmet/HDU alignment was no longer in production or available. Proper helmet/HDU alignment is critical to position the right eye in the small HDU eye box to obtain image alignment and full field of view (FOV). The initial approach of the PM to developing a helmet/HDU fitting device (Mock HDU) was to duplicate the optical characteristics of the current tactical HDU using less complex optics. However, the results produced questionable alignment, FOV, and distortion issues, with cost and development time overruns. After evaluating the Mock HDU, USAARL proposed a cost effective, less complex optical design called the Helmet/HDU Alignment Tool (HAT). This paper will show the development, components, and evaluations of the HAT compared to the current flashlight HDU simulator device. The laboratory evaluations included FOV measurements and alignment accuracies compared to tactical HDUs. The Apache helmet fitter technicians and Apache pilots compared the HAT to the current flashlight based HDU and ranked the HAT superior.

  11. Simrank: Rapid and sensitive general-purpose k-mer search tool

    Directory of Open Access Journals (Sweden)

    Brodie Eoin L

    2011-04-01

    Full Text Available Abstract Background Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project http://nihroadmap.nih.gov/hmp. Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Results Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Conclusions Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.

  12. MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences

    OpenAIRE

    Schwartz, Scott; Elnitski, Laura; Li, Mei; Weirauch, Matt; Riemer, Cathy; Smit, Arian; Green, Eric D; Hardison, Ross C.; Miller, Webb

    2003-01-01

    Analysis of multiple sequence alignments can generate important, testable hypotheses about the phylogenetic history and cellular function of genomic sequences. We describe the MultiPipMaker server, which aligns multiple, long genomic DNA sequences quickly and with good sensitivity (available at http://bio.cse.psu.edu/ since May 2001). Alignments are computed between a contiguous reference sequence and one or more secondary sequences, which can be finished or draft sequence. The outputs includ...

  13. The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Lyngsø, Rune B.; Gorodkin, Jan

    2005-01-01

    FOLDALIGN is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of FOLDALIGN. The server can be used to scan two sequences for a common structural R...... motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. the web server can be accessed at http://foldalign.kvl.dk...

  14. Semantic Search of Tools for Collaborative Learning with the Ontoolsearch System

    Science.gov (United States)

    Vega-Gorgojo, Guillermo; Bote-Lorenzo, Miguel L.; Asensio-Perez, Juan I.; Gomez-Sanchez, Eduardo; Dimitriadis, Yannis A.; Jorrin-Abellan, Ivan M.

    2010-01-01

    This paper introduces Ontoolsearch, a new search system that can be employed by educators in order to find suitable tools for supporting collaborative learning settings. Current tool search facilities commonly allow simple keyword searches, limiting the accuracy of obtained results. In contrast, Ontoolsearch supports semantic querying of tool…

  15. The Theory of Planned Behaviour Applied to Search Engines as a Learning Tool

    Science.gov (United States)

    Liaw, Shu-Sheng

    2004-01-01

    Search engines have been developed for helping learners to seek online information. Based on theory of planned behaviour approach, this research intends to investigate the behaviour of using search engines as a learning tool. After factor analysis, the results suggest that perceived satisfaction of search engine, search engines as an information…

  16. The usability of semantic search tools: a review

    OpenAIRE

    Uren, Victoria; Lei, Yuangui; Lopez, Vanessa; Liu, Haiming; Motta, Enrico; Giordanino, Marina

    2007-01-01

    The goal of semantic search is to improve on traditional search methods by exploiting the semantic metadata. In this paper, we argue that supporting iterative and exploratory search modes is important to the usability of all search systems. We also identify the types of semantic queries the users need to make, the issues concerning the search environment and the problems that are intrinsic to semantic search in particular. We then review the four modes of user interaction in existing semantic...

  17. A magnetically actuated cellular strain assessment tool for quantitative analysis of strain induced cellular reorientation and actin alignment

    Science.gov (United States)

    Khademolhosseini, F.; Liu, C.-C.; Lim, C. J.; Chiao, M.

    2016-08-01

    Commercially available cell strain tools, such as pneumatically actuated elastomer substrates, require special culture plates, pumps, and incubator setups. In this work, we present a magnetically actuated cellular strain assessment tool (MACSAT) that can be implemented using off-the-shelf components and conventional incubators. We determine the strain field on the MACSAT elastomer substrate using numerical models and experimental measurements and show that a specific region of the elastomer substrate undergoes a quasi-uniaxial 2D stretch, and that cells confined to this region of the MACSAT elastomer substrate undergo tensile, compressive, or zero axial strain depending on their angle of orientation. Using the MACSAT to apply cyclic strain on endothelial cells, we demonstrate that actin filaments within the cells reorient away from the stretching direction, towards the directions of minimum axial strain. We show that the final actin orientation angles in strained cells are spread over a region of compressive axial strain, confirming previous findings on the existence of a varied pre-tension in the actin filaments of the cytoskeleton. We also demonstrate that strained cells exhibit distinctly different values of actin alignment coherency compared to unstrained cells and therefore propose that this parameter, i.e., the coherency of actin alignment, can be used as a new readout to determine the occurrence/extent of actin alignment in cell strain experiments. The tools and methods demonstrated in this study are simple and accessible and can be easily replicated by other researchers to study the strain response of other adherent cells.

  18. 4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

    Directory of Open Access Journals (Sweden)

    Schultz Jörg

    2006-11-01

    Full Text Available Abstract Background In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database, we are faced with the problem to handle sequences and their associated secondary structures synchronously. Results 4SALE fills this gap. The application allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis. Conclusion 4SALE, which provides an user-friendly and intuitive interface, is a comprehensive toolbox for RNA analysis based on sequence and secondary structure information. The program connects sequence and structure databases like the ITS2 Database to phylogeny programs as for example the CBCAnalyzer. 4SALE is written in JAVA and therefore platform independent. The software is freely available and distributed from the website at http://4sale.bioapps.biozentrum.uni-wuerzburg.de

  19. Impact of gravitational radiation higher order modes on single aligned-spin gravitational wave searches for binary black holes

    CERN Document Server

    Bustillo, Juan Calderón; Sintes, Alicia M; Püerrer, Michael

    2015-01-01

    Current template-based gravitational wave searches for compact binary coalescences (CBC) use waveform models that neglect the higher order modes content of the gravitational radiation emitted, considering only the quadrupolar $(\\ell,|m|)=(2,2)$ modes. We study the effect of such a neglection for the case of aligned-spin CBC searches for equal-spin (and non-spinning) binary black holes in the context of two versions of Advanced LIGO: the upcoming 2015 version, known as early Advanced LIGO (eaLIGO) and its Zero-Detuned High Energy Power version, that we will refer to as Advanced LIGO (AdvLIGO). In addition, we study the case of a non-spinning search for initial LIGO (iLIGO). We do this via computing the effectualness of the aligned-spin SEOBNRv1 ROM waveform family, which only considers quadrupolar modes, towards hybrid post-Newtonian/Numerical Relativity waveforms which contain higher order modes. We find that for all LIGO versions, losses of more than $10\\%$ of events occur for mass ratio $q\\geq6$ and $M \\geq...

  20. Google vs. the Library (Part II): Student Search Patterns and Behaviors When Using Google and a Federated Search Tool

    Science.gov (United States)

    Georgas, Helen

    2014-01-01

    This study examines the information-seeking behavior of undergraduate students within a research context. Student searches were recorded while the participants used Google and a library (federated) search tool to find sources (one book, two articles, and one other source of their choosing) for a selected topic. The undergraduates in this study…

  1. DMMW: A tool for multi-wavelength dark matter searches

    International Nuclear Information System (INIS)

    The level of emission expected from Dark Matter annihilation at radio frequencies, UV and at X-ray frequencies is comparable, and thus complementary, to searches in gamma rays with Fermi-LAT. However, unlike the prompt gamma-ray emission, the secondary inverse Compton, bremsstrahlung and synchrotron emission from leptons depends on the transport setup and the astrophysical properties of the object under consideration. At the same time Cosmic Ray electrons and positrons, as well as protons form a background which is subject to the same transport model uncertainties. Here we present first results from DMMW (Dark Matter Multi-Wavelength), a tool which is capable of simultaneously fitting the multi-wavelength emission spectrum of a given object for generic Dark Matter models, density distributions and Cosmic Ray transport setups. DMMW allows the user to make reliable predictions about the radio, UV, X-ray and soft gamma-ray emission associated with the relativistic electrons and positrons produced in Dark Matter annihilation, as well as the relativistic electrons, positrons and protons produced in Cosmic Ray sources and Cosmic Ray interactions with the gas. The stable charged annihilation products are propagated in the same framework as the Cosmic Rays, thus allowing the user to probe different transport setups and self-consistently constrain a possible signal from Dark Matter Annihilation from radio to soft gamma-rays.

  2. Search Engine : an effective tool for exploring the Internet

    OpenAIRE

    Ranasinghe, W.M. Tharanga Dilruk

    2006-01-01

    The Internet has become the largest source of information. Today, millions of Websites exist and this number continuous to grow. Finding the right information at the right time is the challenge in the Internet age. Search engine is searchable database which allows locating the information on the Internet by submitting the keywords. Search engines can be divided into two categories as the Individual and Meta Search engines. This article discusses the features of these search engines in detail.

  3. Web Usage Mining Analysis of Federated Search Tools for Egyptian Scholars

    Science.gov (United States)

    Mohamed, Khaled A.; Hassan, Ahmed

    2008-01-01

    Purpose: This paper aims to examine the behaviour of the Egyptian scholars while accessing electronic resources through two federated search tools. The main purpose of this article is to provide guidance for federated search tool technicians and support teams about user issues, including the need for training. Design/methodology/approach: Log…

  4. Multiple Sequence Alignments as Tools for Protein Structure and Function Prediction

    OpenAIRE

    2003-01-01

    Multiple sequence alignments have much to offer to the understanding of protein structure, evolution and function. We are developing approaches to use this information in predicting protein-binding specificity, intra-protein and protein-protein interactions, and in reconstructing protein interaction networks.

  5. Multiple Sequence Alignments as Tools for Protein Structure and Function Prediction

    Directory of Open Access Journals (Sweden)

    Alfonso Valencia

    2006-04-01

    Full Text Available Multiple sequence alignments have much to offer to the understanding of protein structure, evolution and function. We are developing approaches to use this information in predicting protein-binding specificity, intra-protein and protein-protein interactions, and in reconstructing protein interaction networks.

  6. Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures.

    Science.gov (United States)

    Hanke, J; Reich, J G

    1996-12-01

    The method of Kohonen maps, a special form of neural networks, was applied as a visualization tool for the analysis of protein sequence similarity. The procedure converts sequence (domains, aligned sequences, segments of secondary structure) into a characteristic signal matrix. This conversion depends on the property or replacement score vector selected by the user. Similar sequences have small distance in the signal space. The trained Kohonen network is functionally equivalent to an unsupervised non-linear cluster analyzer. Protein families, or aligned sequences, or segments of similar secondary structure, aggregate as clusters, and their proximity may be inspected on a color screen or on paper. Pull-down menus permit access to background information in the established text-oriented way. PMID:9021261

  7. Genetic-Algorithm Tool For Search And Optimization

    Science.gov (United States)

    Wang, Lui; Bayer, Steven

    1995-01-01

    SPLICER computer program used to solve search and optimization problems. Genetic algorithms adaptive search procedures (i.e., problem-solving methods) based loosely on processes of natural selection and Darwinian "survival of fittest." Algorithms apply genetically inspired operators to populations of potential solutions in iterative fashion, creating new populations while searching for optimal or nearly optimal solution to problem at hand. Written in Think C.

  8. The video browser showdown: a live evaluation of interactive video search tools

    OpenAIRE

    Schoeffmann, Klaus; Ahlstroehm, David; Bailer, Werner; Cobarzan, Claudiu; Hopfgartner, Frank; McGuinness, Kevin; Gurrin, Cathal; Frisson, Christian; Le, Duy-Dinh; Del Fabro, Manfred; Bai, Hongliang; Weiss, Wolfgang

    2014-01-01

    The Video Browser Showdown evaluates the performance of exploratory video search tools on a common data set in a common environment and in presence of the audience. The main goal of this competition is to enable researchers in the field of interactive video search to directly compare their tools at work. In this paper, we present results from the second Video Browser Showdown (VBS2013) and describe and evaluate the tools of all participating teams in detail. The evaluation results give insigh...

  9. Open innovation and organizational alignment : a contingency analysis of external search strategies for innovation performance

    OpenAIRE

    Wagner, Philipp

    2013-01-01

    The systematic utilization of external knowledge for innovation purposes, hence open innovation, has received great attention in research and management practice in recent years. Extant research has shown that firms can attain great benefits from searching for innovation relevant knowledge and ideas outside their organizational boundaries. A recent conceptualization of open innovation has differentiated firms’ external search activities with regard to the breadth and depth of the respective e...

  10. Ready Reference Tools: EBSCO Topic Search and SIRS Researcher.

    Science.gov (United States)

    Goins, Sharon; Dayment, Lu

    1998-01-01

    Discussion of ready reference and current events collections in high school libraries focuses on a comparison of two CD-ROM services, EBSCO Topic Search and the SIRS Researcher. Considers licensing; access; search strategies; viewing articles; currency; printing; added value features; and advantages of CD-ROMs. (LRW)

  11. Impact of gravitational radiation higher order modes on single aligned-spin gravitational wave searches for binary black holes

    Science.gov (United States)

    Calderón Bustillo, Juan; Husa, Sascha; Sintes, Alicia M.; Pürrer, Michael

    2016-04-01

    Current template-based gravitational wave searches for compact binary coalescences use waveform models that omit the higher order modes content of the gravitational radiation emitted, considering only the quadrupolar (ℓ,|m |)=(2 ,2 ) modes. We study the effect of such omission for the case of aligned-spin compact binary coalescence searches for equal-spin (and nonspinning) binary black holes in the context of two versions of Advanced LIGO: the upcoming 2015 version, known as early Advanced LIGO (eaLIGO) and its zero-detuned high-energy power version, which we will refer to as Advanced LIGO (AdvLIGO). In addition, we study the case of a nonspinning search for initial LIGO (iLIGO). We do this via computing the effectualness of the aligned-spin SEOBNRv1 reduced order model waveform family, which only considers quadrupolar modes, toward hybrid post-Newtonian/numerical relativity waveforms which contain higher order modes. We find that for all LIGO versions losses of more than 10% of events occur in the case of AdvLIGO for mass ratio q ≥6 and total mass M ≥100 M⊙ due to the omission of higher modes, this region of the parameter space being larger for eaLIGO and iLIGO. Moreover, while the maximum event loss observed over the explored parameter space for AdvLIGO is of 15% of events, for iLIGO and eaLIGO, this increases up to (39,23)%. We find that omission of higher modes leads to observation-averaged systematic parameter biases toward lower spin, total mass, and chirp mass. For completeness, we perform a preliminar, nonexhaustive comparison of systematic biases to statistical errors. We find that, for a given signal-to-noise ratio, systematic biases dominate over statistical errors at much lower total mass for eaLIGO than for AdvLIGO.

  12. Aligning Web-Based Tools to the Research Process Cycle: A Resource for Collaborative Research Projects

    Science.gov (United States)

    Price, Geoffrey P.; Wright, Vivian H.

    2012-01-01

    Using John Creswell's Research Process Cycle as a framework, this article describes various web-based collaborative technologies useful for enhancing the organization and efficiency of educational research. Visualization tools (Cacoo) assist researchers in identifying a research problem. Resource storage tools (Delicious, Mendeley, EasyBib)…

  13. CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping

    Directory of Open Access Journals (Sweden)

    Shi Weisong

    2011-06-01

    Full Text Available Abstract Background Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS. However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues. Consequently, it has been adopted by many organizations recently, and the initial results are very promising. However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc., in on-site software such as RMAP or BS Seeker. In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are inefficient. Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface. Results To urge the trend of using Cloud technologies in genomics and prepare for advances in second- and third-generation DNA sequencing, we have built a Hadoop MapReduce-based application, CloudAligner, which achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface. It was also designed to be able to deal with long sequences. The performance gain of CloudAligner over Cloud-based counterparts (35 to 80% mainly comes from the omission of the reduce phase. In comparison to local-based approaches, the performance gain of CloudAligner is from the partition and parallel processing of the huge reference genome as well as the reads. The source code of CloudAligner is available at http

  14. Evaluation of an open source tool for indexing and searching enterprise radiology and pathology reports

    Science.gov (United States)

    Kim, Woojin; Boonn, William

    2010-03-01

    Data mining of existing radiology and pathology reports within an enterprise health system can be used for clinical decision support, research, education, as well as operational analyses. In our health system, the database of radiology and pathology reports exceeds 13 million entries combined. We are building a web-based tool to allow search and data analysis of these combined databases using freely available and open source tools. This presentation will compare performance of an open source full-text indexing tool to MySQL's full-text indexing and searching and describe implementation procedures to incorporate these capabilities into a radiology-pathology search engine.

  15. PICO, PICOS and SPIDER: a comparison study of specificity and sensitivity in three search tools for qualitative systematic reviews

    OpenAIRE

    Chew-Graham, CA

    2014-01-01

    Background Qualitative systematic reviews are increasing in popularity in evidence based health care. Difficulties have been reported in conducting literature searches of qualitative research using the PICO search tool. An alternative search tool, entitled SPIDER, was recently developed for more effective searching of qualitative research, but remained untested beyond its development team. Methods In this article we tested the ‘SPIDER’ search tool in a systematic narrative review of qualitati...

  16. Data governance tools evaluation criteria, big data governance, and alignment with enterprise data management

    CERN Document Server

    Soares, Sunil

    2015-01-01

    Data governance programs often start off using programs such as Microsoft Excel and Microsoft SharePoint to document and share data governance artifacts. But these tools often lack critical functionality. Meanwhile, vendors have matured their data governance offerings to the extent that today's organizations need to consider tools as a critical component of their data governance programs. In this book, data governance expert Sunil Soares reviews the Enterprise Data Management (EDM) reference architecture and discusses key data governance tasks that can be automated by tools for business glossa

  17. Evaluation and Comparison of a Large Machine Tool Structure with ISO Standard Alignment Tests

    OpenAIRE

    Myers, Alan; Barrans, Simon; Longstaff, Andrew P.; Fletcher, Simon; Ford, Derek G.

    2009-01-01

    In order to satisfactorily machine precision components it is necessary for machine tools to be able to achieve extremely high levels of geometric accuracy. This requires their structures to be extremely rigid such that deflections caused by self weight and traversing of the moving elements do not induce distortions that exceed the required tolerances of the components which are manufactured by the machines. To aid this aspect of machine tool technology, a range of standards...

  18. Search for signatures of magnetically-induced alignment in the arrival directions measured by the Pierre Auger Observatory

    CERN Document Server

    Abreu, P; Ahn, E J; Albuquerque, I F M; Allard, D; Allekotte, I; Allen, J; Allison, P; Castillo, J Alvarez; Alvarez-Muñiz, J; Ambrosio, M; Aminaei, A; Anchordoqui, L; Andringa, S; Antičić, T; Anzalone, A; Aramo, C; Arganda, E; Arqueros, F; Asorey, H; Assis, P; Aublin, J; Ave, M; Avenier, M; Avila, G; Bäcker, T; Balzer, M; Barber, K B; Barbosa, A F; Bardenet, R; Barroso, S L C; Baughman, B; Bäuml, J; Beatty, J J; Becker, B R; Becker, K H; Bellétoile, A; Bellido, J A; BenZvi, S; Berat, C; Bertou, X; Biermann, P L; Billoir, P; Blanco, F; Blanco, M; Bleve, C; Blümer, H; Boháčová, M; Boncioli, D; Bonifazi, C; Bonino, R; Borodai, N; Brack, J; Brogueira, P; Brown, W C; Bruijn, R; Buchholz, P; Bueno, A; Burton, R E; Caballero-Mora, K S; Caramete, L; Caruso, R; Castellina, A; Catalano, O; Cataldi, G; Cazon, L; Cester, R; Chauvin, J; Cheng, S H; Chiavassa, A; Chinellato, J A; Chou, A; Chudoba, J; Clay, R W; Coluccia, M R; Conceição, R; Contreras, F; Cook, H; Cooper, M J; Coppens, J; Cordier, A; Coutu, S; Covault, C E; Creusot, A; Criss, A; Cronin, J; Curutiu, A; Dagoret-Campagne, S; Dallier, R; Dasso, S; Daumiller, K; Dawson, B R; de Almeida, R M; De Domenico, M; De Donato, C; de Jong, S J; De La Vega, G; Junior, W J M de Mello; Neto, J R T de Mello; De Mitri, I; de Souza, V; de Vries, K D; Decerprit, G; del Peral, L; del Río, M; Deligny, O; Dembinski, H; Dhital, N; Di Giulio, C; Diaz, J C; Castro, M L Díaz; Diep, P N; Dobrigkeit, C; Docters, W; D'Olivo, J C; Dong, P N; Dorofeev, A; Anjos, J C dos; Dova, M T; D'Urso, D; Dutan, I; Ebr, J; Engel, R; Erdmann, M; Escobar, C O; Espadanal, J; Etchegoyen, A; Luis, P Facal San; Tapia, I Fajardo; Falcke, H; Farrar, G; Fauth, A C; Fazzini, N; Ferguson, A P; Ferrero, A; Fick, B; Filevich, A; Filipčič, A; Fliescher, S; Fracchiolla, C E; Fraenkel, E D; Fröhlich, U; Fuchs, B; Gaior, R; Gamarra, R F; Gambetta, S; García, B; Gámez, D García; Garcia-Pinto, D; Gascon, A; Gemmeke, H; Gesterling, K; Ghia, P L; Giaccari, U; Giller, M; Glass, H; Gold, M S; Golup, G; Albarracin, F Gomez; Berisso, M Gómez; Gonçalves, P; Gonzalez, D; Gonzalez, J G; Gookin, B; Góra, D; Gorgi, A; Gouffon, P; Gozzini, S R; Grashorn, E; Grebe, S; Griffith, N; Grigat, M; Grillo, A F; Guardincerri, Y; Guarino, F; Guedes, G P; Guzman, A; Hague, J D; Hansen, P; Harari, D; Harmsma, S; Harton, J L; Haungs, A; Hebbeker, T; Heck, D; Herve, A E; Hojvat, C; Hollon, N; Holmes, V C; Homola, P; Hörandel, J R; Horneffer, A; Hrabovský, M; Huege, T; Insolia, A; Ionita, F; Italiano, A; Jarne, C; Jiraskova, S; Josebachuili, M; Kadija, K; Kampert, K H; Karhan, P; Kasper, P; Kégl, B; Keilhauer, B; Keivani, A; Kelley, J L; Kemp, E; Kieckhafer, R M; Klages, H O; Kleifges, M; Kleinfeller, J; Knapp, J; Koang, D -H; Kotera, K; Krohm, N; Krömer, O; Kruppke-Hansen, D; Kuehn, F; Kuempel, D; Kulbartz, J K; Kunka, N; La Rosa, G; Lachaud, C; Lautridou, P; Leão, M S A B; Lebrun, D; Lebrun, P; de Oliveira, M A Leigui; Lemiere, A; Letessier-Selvon, A; Lhenry-Yvon, I; Link, K; López, R; Agüera, A Lopez; Louedec, K; Bahilo, J Lozano; Lu, L; Lucero, A; Ludwig, M; Lyberis, H; Maccarone, M C; Macolino, C; Maldera, S; Mandat, D; Mantsch, P; Mariazzi, A G; Marin, J; Marin, V; Maris, I C; Falcon, H R Marquez; Marsella, G; Martello, D; Martin, L; Martinez, H; Bravo, O Martínez; Mathes, H J; Matthews, J; Matthews, J A J; Matthiae, G; Maurizio, D; Mazur, P O; Medina-Tanco, G; Melissas, M; Melo, D; Menichetti, E; Menshikov, A; Mertsch, P; Meurer, C; Mićanović, S; Micheletti, M I; Miller, W; Miramonti, L; Molina-Bueno, L; Mollerach, S; Monasor, M; Ragaigne, D Monnier; Montanet, F; Morales, B; Morello, C; Moreno, E; Moreno, J C; Morris, C; Mostafá, M; Moura, C A; Mueller, S; Muller, M A; Müller, G; Münchmeyer, M; Mussa, R; Navarra, G; Navarro, J L; Navas, S; Necesal, P; Nellen, L; Nelles, A; Neuser, J; Nhung, P T; Niemietz, L; Nierstenhoefer, N; Nitz, D; Nosek, D; Nožka, L; Nyklicek, M; Oehlschläger, J; Olinto, A; Oliva, P; Olmos-Gilbaja, V M; Ortiz, M; Pacheco, N; Selmi-Dei, D Pakk; Palatka, M; Pallotta, J; Palmieri, N; Parente, G; Parizot, E; Parra, A; Parsons, R D; Pastor, S; Paul, T; Pech, M; Pȩkala, J; Pelayo, R; Pepe, I M; Perrone, L; Pesce, R; Petermann, E; Petrera, S; Petrinca, P; Petrolini, A; Petrov, Y; Petrovic, J; Pfendner, C; Phan, N; Piegaia, R; Pierog, T; Pieroni, P; Pimenta, M; Pirronello, V; Platino, M; Ponce, V H; Pontz, M; Privitera, P; Prouza, M; Quel, E J; Querchfeld, S; Rautenberg, J; Ravel, O; Ravignani, D; Revenu, B; Ridky, J; Riggi, S; Risse, M; Ristori, P; Rivera, H; Rizi, V; Roberts, J; Robledo, C; de Carvalho, W Rodrigues; Rodriguez, G; Martino, J Rodriguez; Rojo, J Rodriguez; Rodriguez-Cabo, I; Rodríguez-Frías, M D; Ros, G; Rosado, J; Rossler, T; Roth, M; Rouillé-d'Orfeuil, B; Roulet, E; Rovero, A C; Rühle, C; Salamida, F; Salazar, H; Salina, G; Sánchez, F; Santo, C E; Santos, E; Santos, E M; Sarazin, F; Sarkar, B; Sarkar, S; Sato, R; Scharf, N; Scherini, V; Schieler, H; Schiffer, P; Schmidt, A; Schmidt, F; Scholten, O; Schoorlemmer, H; Schovancova, J; Schovánek, P; Schröder, F; Schulte, S; Schuster, D; Sciutto, S J; Scuderi, M; Segreto, A; Settimo, M; Shadkam, A; Shellard, R C; Sidelnik, I; Sigl, G; Lopez, H H Silva; Śmiałkowski, A; Šmída, R; Snow, G R; Sommers, P; Sorokin, J; Spinka, H; Squartini, R; Stanic, S; Stapleton, J; Stasielak, J; Stephan, M; Strazzeri, E; Stutz, A; Suarez, F; Suomijärvi, T; Supanitsky, A D; Šuša, T; Sutherland, M S; Swain, J; Szadkowski, Z; Szuba, M; Tamashiro, A; Tapia, A; Tartare, M; Taşcău, O; Ruiz, C G Tavera; Tcaciuc, R; Tegolo, D; Thao, N T; Thomas, D; Tiffenberg, J; Timmermans, C; Tiwari, D K; Tkaczyk, W; Peixoto, C J Todero; Tomé, B; Tonachini, A; Travnicek, P; Tridapalli, D B; Tristram, G; Trovato, E; Tueros, M; Ulrich, R; Unger, M; Urban, M; Galicia, J F Valdés; Valiño, I; Valore, L; Berg, A M van den; Varela, E; Cárdenas, B Vargas; Vázquez, J R; Vázquez, R A; Veberič, D; Verzi, V; Vicha, J; Videla, M; Villaseñor, L; Wahlberg, H; Wahrlich, P; Wainberg, O; Walz, D; Warner, D; Watson, A A; Weber, M; Weidenhaupt, K; Weindl, A; Westerhoff, S; Whelan, B J; Wieczorek, G; Wiencke, L; Wilczyńska, B; Wilczyński, H; Will, M; Williams, C; Winchen, T; Winnick, M G; Wommer, M; Wundheiler, B; Yamamoto, T; Yapici, T; Younk, P; Yuan, G; Yushkov, A; Zamorano, B; Zas, E; Zavrtanik, D; Zavrtanik, M; Zaw, I; Zepeda, A; Silva, M Zimbres; Ziolkowski, M; 10.1016/j.astropartphys.2011.10.004

    2011-01-01

    We present the results of an analysis of data recorded at the Pierre Auger Observatory in which we search for groups of directionally-aligned events (or `multiplets') which exhibit a correlation between arrival direction and the inverse of the energy. These signatures are expected from sets of events coming from the same source after having been deflected by intervening coherent magnetic fields. The observation of several events from the same source would open the possibility to accurately reconstruct the position of the source and also measure the integral of the component of the magnetic field orthogonal to the trajectory of the cosmic rays. We describe the largest multiplets found and compute the probability that they appeared by chance from an isotropic distribution. We find no statistically significant evidence for the presence of multiplets arising from magnetic deflections in the present data.

  19. Use of the smartt interferometer as an alignement tool for infrared laser systems

    International Nuclear Information System (INIS)

    The ability to minimize the pointing and focusing errors at the focal plane is crucial in many applications involving infrared laser systems. This is particularly the case for systems involving multiple beams reaching the focal plane, as in the case of the LASL CO2 laser fusion systems. For example, the LASL Helios CO2 Laser Fusion System has eight 34-cm diameter beams each with an f number of approximately 2.4 coming to focus, the last element being an off-aperture parabola with a focal length of approximately 77.3 cm. The design tolerance for pointing accuracy is + 25 microns and for focusing acccuracy is +- 50 microns for the Helios system. The Smartt interferometer shows promise of not only evaluating the optical quality of the beam, but it can be used to align the beam to the tolerance levels stated above. This paper describes the procedure, as well as experimental results obtained, which show that pointing accuracies of +-12.5 microns and focusing accuracies of +- 25 microns are obtained at the focus of a CO2 laser beam in a setup which duplicates the target regionn of the Helios CO2 Laser Fusion System

  20. What limits tool use in nonhuman primates? Insights from tufted capuchin monkeys (Sapajus spp.) and chimpanzees (Pan troglodytes) aligning three-dimensional objects to a surface.

    Science.gov (United States)

    la Cour, L T; Stone, B W; Hopkins, W; Menzel, C; Fragaszy, Dorothy M

    2014-01-01

    Perceptuomotor functions that support using hand tools can be examined in other manipulation tasks, such as alignment of objects to surfaces. We examined tufted capuchin monkeys' and chimpanzees' performance at aligning objects to surfaces while managing one or two spatial relations to do so. We presented six subjects of each species with a single stick to place into a groove, two sticks of equal length to place into two grooves, or two sticks joined as a T to place into a T-shaped groove. Tufted capuchins and chimpanzees performed equivalently on these tasks, aligning the straight stick to within 22.5° of parallel to the groove in approximately half of their attempts to place it, and taking more attempts to place the T stick than two straight sticks. The findings provide strong evidence that tufted capuchins and chimpanzees do not reliably align even one prominent axial feature of an object to a surface, and that managing two concurrent allocentric spatial relations in an alignment problem is significantly more challenging to them than managing two sequential relations. In contrast, humans from 2 years of age display very different perceptuomotor abilities in a similar task: they align sticks to a groove reliably on each attempt, and they readily manage two allocentric spatial relations concurrently. Limitations in aligning objects and in managing two or more relations at a time significantly constrain how nonhuman primates can use hand tools. PMID:23820935

  1. Using evolutionary tools to search for novel psychoactive plants

    DEFF Research Database (Denmark)

    Rønsted, Nina; Halse-Gramkow, Morten; Ernst, Madeleine;

    2016-01-01

    Bioprospecting is the search for valuable products from natural sources. Given that most species are poorly known, a key question is where to search. Ethnodirected bioprospecting approaches use traditional knowledge in the process of selecting plants to screen for desired properties. A...... complementary approach is to utilise phylogenetic analyses based on traditional uses or known chemistry to identify lineages in which desired properties are most likely to be found. Novel discoveries of plant bioactivity from these approaches can aid the development of treatments for diseases with unmet medical...... needs. For example, neurological disorders are a growing concern, and psychoactive plants used in traditional medicine may provide botanical sources for bioactivity relevant for treating diseases related to the brain and nervous system. However, no systematic study has explored the diversity and...

  2. Searching for Sentient Design Tools for Game Development

    DEFF Research Database (Denmark)

    Liapis, Antonios

    a large volume of game content or to reduce designer effort by automating the mechanizable aspects of content creation, such as feasibility checking. However elaborate the type of content such tools can create, they remain subservient to their human developers/creators (who have tightly designed all...... their generative algorithms) and to their human users (who must take all design decisions), respectively. This thesis argues that computers can be creative partners to human designers rather than mere slaves; game design tools can be aware of designer intentions, preferences and routines, and can accommodate them...... or even subvert them. This thesis presents Sentient Sketchbook, a tool for designing game level abstractions of different game genres, which assists the level designer as it automatically tests maps for playability constraints, evaluates and displays the map's gameplay properties and creates alternatives...

  3. Automatic tool alignment in a backscatter x-ray scanning system

    Energy Technology Data Exchange (ETDEWEB)

    Garretson, Justin; Hobart, Clinton G.; Gladwell, Thomas S.; Monda, Mark J.

    2015-06-16

    Technologies pertaining to backscatter x-ray scanning systems are described herein. The backscatter x-ray scanning system includes an x-ray source, which directs collimated x-rays along a plurality of output vectors towards a target. A detector detects diffusely reflected x-rays subsequent to respective collimated x-rays impacting the target, and outputs signals indicative of parameters of the detected x-rays. An image processing system generates an x-ray image based upon parameters of the detected x-rays, wherein each pixel in the image corresponds to a respective output vector. A user selects a particular portion of the image, and a tool is positioned such that its directional axis is coincident with the output vector corresponding to at least one pixel in the portion of the image.

  4. Global search tool for the Advanced Photon Source Integrated Relational Model of Installed Systems (IRMIS) database

    International Nuclear Information System (INIS)

    The Integrated Relational Model of Installed Systems (IRMIS) is a relational database tool that has been implemented at the Advanced Photon Source to maintain an updated account of approximately 600 control system software applications, 400,000 process variables, and 30,000 control system hardware components. To effectively display this large amount of control system information to operators and engineers, IRMIS was initially built with nine Web-based viewers: Applications Organizing Index, IOC, PLC, Component Type, Installed Components, Network, Controls Spares, Process Variables, and Cables. However, since each viewer is designed to provide details from only one major category of the control system, the necessity for a one-stop global search tool for the entire database became apparent. The user requirements for extremely fast database search time and ease of navigation through search results led to the choice of Asynchronous JavaScript and XML (AJAX) technology in the implementation of the IRMIS global search tool. Unique features of the global search tool include a two-tier level of displayed search results, and a database data integrity validation and reporting mechanism.

  5. STELLAR: fast and exact local alignments

    Directory of Open Access Journals (Sweden)

    Weese David

    2011-10-01

    Full Text Available Abstract Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de.

  6. Search for Anisotropic Light Propagation as a Function of Laser Beam Alignment Relative to the Earth's Velocity Vector

    Directory of Open Access Journals (Sweden)

    Navia C. E.

    2007-01-01

    Full Text Available A laser diffraction experiment was conducted to study light propagation in air. The experiment is easy to reproduce and it is based on simple optical principles. Two optical sensors (segmented photo-diodes are used for measuring the position of diffracted light spots with a precision better than 0.1 μ m. The goal is to look for signals of anisotropic light propagation as function of the laser beam alignment to the Earth’s motion (solar barycenter motion obtained by COBE. Two raster search techniques have been used. First, a laser beam fixed in the laboratory frame scans in space due to Earth’s rotation. Second, a laser beam mounted on a turntable system scans actively in space by turning the table. The results obtained with both methods show that the course of light rays are affected by the motion of the Earth, and a predominant first order quantity with a Δ c/c = − β (1 + 2 a cos θ signature with ˉ a = − 0.393 ± 0.032 describes well the experimental results. This result differs in amount of 21% from the Special Relativity Theory prediction and that supplies the value of a = − 1 2 (isotropy.

  7. Search for anisotropic light propagation as a function of laser beam alignment relative to the Earth's velocity vector

    CERN Document Server

    Navia, C E; Franceschini, D F; Robba, M B; Tsui, K H

    2006-01-01

    A laser diffraction experiment was conducted to study light propagation in air. The experiment is easy to reproduce and it is based on simple optical principles. Two optical sensors (segmented photo-diodes) are used for measuring the position of diffracted light spots with a precision better than $0.1 \\mu m$. The goal is to look for signals of anisotropic light propagation as function of the laser beam alignment to the Earth's motion (solar barycenter motion) obtained by COBE. Two raster search techniques have been used. First, a fixed laser beam in the laboratory frame that scans due to Earth's rotation. Second, an active rotation of the laser beam on a turntable system. The results obtained with both methods show that the course of the light rays are affected by the motion of the Earth, and a predominant quantity of first order with a $\\Delta c/c=-\\beta (1+2a)\\cos \\theta$ signature with $a=-0.4106\\pm 0.0225$ describes well the experimental results. This result differs in a amount of 18% from the Special Rel...

  8. Search for bright nearby M dwarfs with Virtual Observatory tools

    CERN Document Server

    Aberasturi, M; Montesinos, B; Gálvez-Ortiz, M C; Solano, E; Martín, E L

    2014-01-01

    Using Virtual Observatory tools, we cross-matched the Carlsberg Meridian 14 and the 2MASS Point Source catalogs to select candidate nearby bright M dwarfs distributed over ~ 25,000 deg^2. Here, we present reconnaissance low-resolution optical spectra for 27 candidates that were observed with the Intermediate Dispersion Spectrograph at the 2.5m Isaac Newton Telescope (R ~ 1600). We derived spectral types from a new spectral index, R, which measures the ratio of fluxes at 7485-7015 A and 7120-7150 A. We also used VOSA, a Virtual Observatory tool for spectral energy distribution fitting, to derive effective temperatures and surface gravities for each candidate. The resulting 27 targets were M dwarfs brighter than J = 10.5 mag, 16 of which were completely new in the Northern hemisphere and 7 of which were located at less than 15 pc. For all of them, we also measured H{\\alpha} and Na I pseudo-equivalent widths, determined photometric distances, and identified the most active stars. The targets with the weakest sod...

  9. Search for bright nearby M dwarfs with virtual observatory tools

    Energy Technology Data Exchange (ETDEWEB)

    Aberasturi, M.; Caballero, J. A.; Montesinos, B.; Gálvez-Ortiz, M. C.; Solano, E.; Martín, E. L. [Centro de Astrobiología (CSIC-INTA), Departamento de Astrofísica, P.O. Box 78, E-28691 Villanueva de la Cañada, Madrid (Spain)

    2014-08-01

    Using Virtual Observatory tools, we cross-matched the Carlsberg Meridian 14 and the 2MASS Point Source catalogs to select candidate nearby bright M dwarfs distributed over ∼25,000 deg{sup 2}. Here, we present reconnaissance low-resolution optical spectra for 27 candidates that were observed with the Intermediate Dispersion Spectrograph at the 2.5 m Isaac Newton Telescope (R≈ 1600). We derived spectral types from a new spectral index, R, which measures the ratio of fluxes at 7485-7015 Å and 7120-7150 Å. We also used VOSA, a Virtual Observatory tool for spectral energy distribution fitting, to derive effective temperatures and surface gravities for each candidate. The resulting 27 targets were M dwarfs brighter than J = 10.5 mag, 16 of which were completely new in the Northern hemisphere and 7 of which were located at less than 15 pc. For all of them, we also measured Hα and Na I pseudo-equivalent widths, determined photometric distances, and identified the most active stars. The targets with the weakest sodium absorption, namely, J0422+2439 (with X-ray and strong Hα emissions), J0435+2523, and J0439+2333, are new members in the young Taurus-Auriga star-forming region based on proper motion, spatial distribution, and location in the color-magnitude diagram, which reopens the discussion on the deficit of M2-4 Taurus stars. Finally, based on proper motion diagrams, we report on a new wide M dwarf binary system in the field, LSPM J0326+3929EW.

  10. Search for bright nearby M dwarfs with virtual observatory tools

    International Nuclear Information System (INIS)

    Using Virtual Observatory tools, we cross-matched the Carlsberg Meridian 14 and the 2MASS Point Source catalogs to select candidate nearby bright M dwarfs distributed over ∼25,000 deg2. Here, we present reconnaissance low-resolution optical spectra for 27 candidates that were observed with the Intermediate Dispersion Spectrograph at the 2.5 m Isaac Newton Telescope (R≈ 1600). We derived spectral types from a new spectral index, R, which measures the ratio of fluxes at 7485-7015 Å and 7120-7150 Å. We also used VOSA, a Virtual Observatory tool for spectral energy distribution fitting, to derive effective temperatures and surface gravities for each candidate. The resulting 27 targets were M dwarfs brighter than J = 10.5 mag, 16 of which were completely new in the Northern hemisphere and 7 of which were located at less than 15 pc. For all of them, we also measured Hα and Na I pseudo-equivalent widths, determined photometric distances, and identified the most active stars. The targets with the weakest sodium absorption, namely, J0422+2439 (with X-ray and strong Hα emissions), J0435+2523, and J0439+2333, are new members in the young Taurus-Auriga star-forming region based on proper motion, spatial distribution, and location in the color-magnitude diagram, which reopens the discussion on the deficit of M2-4 Taurus stars. Finally, based on proper motion diagrams, we report on a new wide M dwarf binary system in the field, LSPM J0326+3929EW.

  11. Search for Bright Nearby M Dwarfs with Virtual Observatory Tools

    Science.gov (United States)

    Aberasturi, M.; Caballero, J. A.; Montesinos, B.; Gálvez-Ortiz, M. C.; Solano, E.; Martín, E. L.

    2014-08-01

    Using Virtual Observatory tools, we cross-matched the Carlsberg Meridian 14 and the 2MASS Point Source catalogs to select candidate nearby bright M dwarfs distributed over ~25,000 deg2. Here, we present reconnaissance low-resolution optical spectra for 27 candidates that were observed with the Intermediate Dispersion Spectrograph at the 2.5 m Isaac Newton Telescope ( {R} \\approx 1600). We derived spectral types from a new spectral index, real, which measures the ratio of fluxes at 7485-7015 Å and 7120-7150 Å. We also used VOSA, a Virtual Observatory tool for spectral energy distribution fitting, to derive effective temperatures and surface gravities for each candidate. The resulting 27 targets were M dwarfs brighter than J = 10.5 mag, 16 of which were completely new in the Northern hemisphere and 7 of which were located at less than 15 pc. For all of them, we also measured Hα and Na I pseudo-equivalent widths, determined photometric distances, and identified the most active stars. The targets with the weakest sodium absorption, namely, J0422+2439 (with X-ray and strong Hα emissions), J0435+2523, and J0439+2333, are new members in the young Taurus-Auriga star-forming region based on proper motion, spatial distribution, and location in the color-magnitude diagram, which reopens the discussion on the deficit of M2-4 Taurus stars. Finally, based on proper motion diagrams, we report on a new wide M dwarf binary system in the field, LSPM J0326+3929EW.

  12. RAG-3D: a search tool for RNA 3D substructures.

    Science.gov (United States)

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-10-30

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D-a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool-designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

  13. FASTERp: A Feature Array Search Tool for Estimating Resemblance of Protein Sequences

    Energy Technology Data Exchange (ETDEWEB)

    Macklin, Derek; Egan, Rob; Wang, Zhong

    2014-03-14

    Metagenome sequencing efforts have provided a large pool of billions of genes for identifying enzymes with desirable biochemical traits. However, homology search with billions of genes in a rapidly growing database has become increasingly computationally impractical. Here we present our pilot efforts to develop a novel alignment-free algorithm for homology search. Specifically, we represent individual proteins as feature vectors that denote the presence or absence of short kmers in the protein sequence. Similarity between feature vectors is then computed using the Tanimoto score, a distance metric that can be rapidly computed on bit string representations of feature vectors. Preliminary results indicate good correlation with optimal alignment algorithms (Spearman r of 0.87, ~;;1,000,000 proteins from Pfam), as well as with heuristic algorithms such as BLAST (Spearman r of 0.86, ~;;1,000,000 proteins). Furthermore, a prototype of FASTERp implemented in Python runs approximately four times faster than BLAST on a small scale dataset (~;;1000 proteins). We are optimizing and scaling to improve FASTERp to enable rapid homology searches against billion-protein databases, thereby enabling more comprehensive gene annotation efforts.

  14. Global alignment optimization strategies, procedures, and tools for the James Webb Space Telescope (JWST) Integrated Science Instrument Module (ISIM)

    Science.gov (United States)

    Bos, Brent J.; Howard, Joseph M.; Young, Philip J.; Gracey, Renee; Seals, Lenward T.; Ohl, Raymond G.

    2012-09-01

    During cryogenic vacuum testing of the James Webb Space Telescope (JWST) Integrated Science Instrument Module (ISIM), the global alignment of the ISIM with respect to the designed interface of the JWST optical telescope element (OTE) will be measured through a series of optical characterization tests. These tests will determine the locations and orientations of the JWST science instrument projected focal surfaces and entrance pupils with respect to their corresponding OTE optical interfaces. Thermal, finite element and optical modeling will then be used to predict the on-orbit optical performance of the observatory. If any optical performance non-compliances are identified, the ISIM will be adjusted to improve its performance. If this becomes necessary, ISIM has a variety of adjustments that can be made. The lengths of the six kinematic mount struts that attach the ISIM to the OTE can be modified and five science instrument focus positions and two pupil positions can be individually adjusted as well. In order to understand how to manipulate the ISIM’s degrees of freedom properly and to prepare for the ISIM flight model testing, we have completed a series of optical-mechanical analyses to develop and identify the best approaches for bringing a non-compliant ISIM Element back into compliance. During this work several unknown misalignment scenarios were produced and the simulated optical performance metrics were input into various mathematical modeling and optimization tools to determine how the ISIM degrees of freedom should be adjusted to provide the best overall optical performance.

  15. The Anatomy of a Small-Scale Document Search Engine Tool: Incorporating a new Ranking Algorithm

    Directory of Open Access Journals (Sweden)

    KAUSTUBH S. RAVAL

    2011-07-01

    Full Text Available A search engine is an information retrieval system to help find out the information contained in documents stored on a computer system. The results provided by this kind of a system are usually in form of a list. Search engines basically work on the concept called ‘Text-Mining’. Text mining is a variation on a field called data mining and refers to the process of deriving high-quality information from unstructured text. In this paper we are going to depict an intelligent agent based search engine tool which takes the input from user in form of keyword and based on the keyword, find out the matching documents and show it to user (in the form of links.This tool uses a new ‘Ranking Algorithm’ to rank the documents.

  16. ExactSearch: a web-based plant motif search tool

    OpenAIRE

    Gunasekara, Chathura; Subramanian, Avinash; Avvari, Janaki Venkata Ram Kumar; Li, Bin; Chen, Su; Wei, Hairong

    2016-01-01

    Background Plant biologists frequently need to examine if a sequence motif bound by a specific transcription or translation factor is present in the proximal promoters or 3′ untranslated regions (3′ UTR) of a set of plant genes of interest. To achieve such a task, plant biologists have to not only identify an appropriate algorithm for motif searching, but also manipulate the large volume of sequence data, making it burdensome to carry out or fulfill. Result In this study, we developed a web p...

  17. Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

    Directory of Open Access Journals (Sweden)

    Richard Wilton

    2015-03-01

    Full Text Available When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU hardware.We followed this approach in implementing a read aligner called Arioc that uses GPU-based parallel sort and reduction techniques to identify high-priority locations where potential alignments may be found. We then carried out a read-by-read comparison of Arioc’s reported alignments with the alignments found by several leading read aligners. With simulated reads, Arioc has comparable or better accuracy than the other read aligners we tested. With human sequencing reads, Arioc demonstrates significantly greater throughput than the other aligners we evaluated across a wide range of sensitivity settings. The Arioc software is available at https://github.com/RWilton/Arioc. It is released under a BSD open-source license.

  18. Google vs. the Library: Student Preferences and Perceptions when Doing Research Using Google and a Federated Search Tool

    Science.gov (United States)

    Georgas, Helen

    2013-01-01

    Federated searching was once touted as the library world's answer to Google, but ten years since federated searching technology's inception, how does it actually compare? This study focuses on undergraduate student preferences and perceptions when doing research using both Google and a federated search tool. Students were asked about their…

  19. Impact of dose evaluation using various gamma tools depending on gird size and searching range

    International Nuclear Information System (INIS)

    The dosimeters for dose measurement have been grown 1D such as farmer ion chamber to 2D like radiochromic film and finally 3D such as polymerizing gels gradually and radiotherapy planning which is complicated and has steep dose gradient such as IMRT is under progress in these days. Therefore, dose evaluation for assuring accuracy about comparison between measured and calculated dose distributions becomes more and more important. It is very important dose distribution is assessed at complex field having sharp gradient such as IMRT, VMAT. The commonly used dose analysis tools are gamma tools that included dose concept and distance concept. Figure 1 shows results of prostate field are similar to that of the wedge field. Therefore, we found pass ratio fell sharply as grid size increased because of gradually bigger gamma value. This study estimated changes of images according to searching range and differences of gamma values in each searching range.As searching ranges became bigger, gamma value also was increased and visible noise of images got worse severely for two models. This study evaluated difference according to gamma models and changes of gamma values according to grid size and searching range. The pass ratio fell down as grid size increased at all gamma models and all fields, however gap between 0.5 mm and 1 mm is not significantly different. For searching range, artifacts of images and gamma values increased when it rose at all gamma models and all fields.

  20. Sequence Searcher: A Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences

    Directory of Open Access Journals (Sweden)

    Upton Chris

    2009-01-01

    Full Text Available Abstract Background Many sequence-searching tools have limiting factors for their use. For example, they may be platform specific, enforce restrictive size limits and sequences to be searched, or only allow searches of one of DNA or protein. Findings We present an easy-to-use, fast, platform-independent tool to search for amino acid or nucleotide patterns within one or many protein or nucleic acid sequences. The user can choose to search for regular expressions or perform a fuzzy search in which a particular number of errors is accepted during matching of a sequence. Positions of mismatches in fuzzy searches are displayed graphically the user. Conclusion SeqS provides an improved feature set and functions as a stand-alone tool or could be integrated into other bioinformatics platforms.

  1. VirusPKT: A Search Tool For Assimilating Assorted Acquaintance For Viruses

    CERN Document Server

    Manicassamy, Jayanthi

    2009-01-01

    Viruses utilize various means to circumvent the immune detection in the biological systems. Several mathematical models have been investigated for the description of viral dynamics in the biological system of human and various other species. One common strategy for evasion and recognition of viruses is, through acquaintance in the systems by means of search engines. In this perspective a search tool have been developed to provide a wider comprehension about the structure and other details on viruses which have been narrated in this paper. This provides an adequate knowledge in evolution and building of viruses, its functions through information extraction from various websites. Apart from this, tool aim to automate the activities associated with it in a self-maintainable, self-sustainable, proactive one which has been evaluated through analysis made and have been discussed in this paper.

  2. VirusPKT: A Search Tool For Assimilating Assorted Acquaintance For Viruses

    Directory of Open Access Journals (Sweden)

    Jayanthi Manicassamy

    2009-11-01

    Full Text Available Viruses utilize various means to circumvent the immune detection in the biological systems. Several mathematical models have been investigated for the description of viral dynamics in the biological system of human and various other species. One common strategy for evasion and recognition of viruses is, through acquaintance in the systems by means of search engines. In this perspective a search tool have been developed to provide a wider comprehension about the structure and other details on viruses which have been narrated in this paper. This provides an adequate knowledge in evolution and building of viruses, its functions through information extraction from various websites. Apart from this, tool aim to automate the activities associated with it in a self-maintainable, self-sustainable, proactive one which has been evaluated through analysis made and have been discussed in this paper.

  3. Federated Search Tools in Fusion Centers : Bridging Databases in the Information Sharing Environment

    OpenAIRE

    Wormet, Jody R.

    2012-01-01

    This research utilized a semi-structured survey instrument delivered to subject matter experts within the national network of fusion centers and employed a constant comparison method to analyze the survey results. This smart practice exploration informed through an appreciative inquiry lens found considerable variation in how fusion centers plan for, gather requirements, select and acquire federated search tools to bridge disparate databases. These findings confirmed the initial hypothesis th...

  4. UniProt Tools.

    Science.gov (United States)

    Pundir, Sangya; Martin, Maria J; O'Donovan, Claire

    2016-01-01

    The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data (UniProt Consortium, 2015). The UniProt Web site receives ∼400,000 unique visitors per month and is the primary means to access UniProt. Along with various datasets that you can search, UniProt provides three main tools. These are the 'BLAST' tool for sequence similarity searching, the 'Align' tool for multiple sequence alignment, and the 'Retrieve/ID Mapping' tool for using a list of identifiers to retrieve UniProtKB proteins and to convert database identifiers from UniProt to external databases or vice versa. This unit provides three basic protocols, three alternate protocols, and two support protocols for using UniProt tools. © 2016 by John Wiley & Sons, Inc. PMID:27010333

  5. Semiautomated improvement of RNA alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Lind-Thomsen, Allan; Knudsen, Bjarne;

    2007-01-01

    We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily...... the SARSE editor makes it a flexible tool to improve all RNA alignments with relatively little human intervention. Online documentation and software are available at (http://sarse.ku.dk)....

  6. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

    OpenAIRE

    Daily, Jeff

    2016-01-01

    Background Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-seque...

  7. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Z. Szillasi and G. Gomez.

    2013-01-01

    When CMS is opened up, major components of the Link and Barrel Alignment systems will be removed. This operation, besides allowing for maintenance of the detector underneath, is needed for making interventions that will reinforce the alignment measurements and make the operation of the alignment system more reliable. For that purpose and also for their general maintenance and recalibration, the alignment components will be transferred to the Alignment Lab situated in the ISR area. For the track-based alignment, attention is focused on the determination of systematic uncertainties, which have become dominant, since now there is a large statistics of muon tracks. This will allow for an improved Monte Carlo misalignment scenario and updated alignment position errors, crucial for high-momentum muon analysis such as Z′ searches.

  8. Use of webcams as tools for alignment and supervision of a Thomson scattering system in the near infrared

    International Nuclear Information System (INIS)

    The alignment stability is a major concern for Thomson scattering systems. Even small angular deviations of the laser beams crossing the plasma lead to a loss of the calibration resulting in unreliable measurements of the electron density profile. For the TCV (Tokamak a Configuration Variable) installation, the beam paths from the laser output to the vacuum chamber are ∼25 m long and include several optical components. In order to monitor the alignment on a regular basis, a set of 9 cameras has been installed at several locations along the beam path. They view the actual laser beam pattern by recording the scattered light from an intercepting optical surface (mirror or window) together with the position of markers used for reference. Small 'webcams' are used for this purpose; they feature adequate intensity response at the laser wavelength of 1.06 μm, are compact, cheap and several units may be connected to a server PC simultaneously. The real-time images from all the cameras are accessible from a Web browser. This installation has proven to be extremely useful in the early detection of alignment problems and to assist the alignment procedure .

  9. RNA secondary structure, an important bioinformatics tool to enhance multiple sequence alignment: a case study (Sordariomycetes, Fungi)

    Czech Academy of Sciences Publication Activity Database

    Réblová, Martina; Réblová, K.

    2013-01-01

    Roč. 12, č. 2 (2013), s. 305-319. ISSN 1617-416X R&D Projects: GA ČR GAP506/12/0038 Institutional support: RVO:67985939 Keywords : 2D structure * 2D mask * alignment Subject RIV: EF - Botanics Impact factor: 1.543, year: 2013

  10. Tool Path Generation for Clean-up Machining of Impeller by Point-searching Based Method

    Institute of Scientific and Technical Information of China (English)

    TANG Ming; ZHANG Dinghua; LUO Ming; WU Baohai

    2012-01-01

    Machining quality of clean-up region has a strong influence on the performances of the impeller.In order to plan clean-up tool paths rapidly and obtain good finish surface quality,an efficient and robust tool path generation method is presented,which employs an approach based on point-searching.The clean-up machining mentioned in this paper is pencil-cut and multilayer fillet-cut for a free-form model with a ball-end cutter.For pencil-cut,the cutter center position can be determined via judging whether it satisfies the distance requirement.After the searching direction and the tracing direction have been determined,by employing the point-searching algorithm with the idea of dichotomy,all the cutter contact (CC) points and cutter location (CL)points can be found and the clean-up boundaries can also be defined rapidly.Then the tool path is generated.Based on the main concept of pencil-cut,a multilayer fillet-cut method is proposed,which utilizes a ball-end cuter with its radius less than the design radius of clean-up region.Using a sequence of intermediate virtual cutters to divide the clean-uP region into several layersand given a cusp-height tolerance for the final layer,then the tool paths for all layers are calculated.Finally,computer implementation is also presented in this paper,and the result shows that the proposed method is feasible.

  11. Protein structural similarity search by Ramachandran codes

    OpenAIRE

    Chang Chih-Hung; Huang Po-Jung; Lo Wei-Cheng; Lyu Ping-Chiang

    2007-01-01

    Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we ai...

  12. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez.

    Since June of 2009, the muon alignment group has focused on providing new alignment constants and on finalizing the hardware alignment reconstruction. Alignment constants for DTs and CSCs were provided for CRAFT09 data reprocessing. For DT chambers, the track-based alignment was repeated using CRAFT09 cosmic ray muons and validated using segment extrapolation and split cosmic tools. One difference with respect to the previous alignment is that only five degrees of freedom were aligned, leaving the rotation around the local x-axis to be better determined by the hardware system. Similarly, DT chambers poorly aligned by tracks (due to limited statistics) were aligned by a combination of photogrammetry and hardware-based alignment. For the CSC chambers, the hardware system provided alignment in global z and rotations about local x. Entire muon endcap rings were further corrected in the transverse plane (global x and y) by the track-based alignment. Single chamber track-based alignment suffers from poor statistic...

  13. Google Sets, Google Suggest, and Google Search History: Three More Tools for the Reference Librarian's Bag of Tricks

    OpenAIRE

    Cirasella, Jill

    2008-01-01

    This article examines the features, quirks, and uses of Google Sets, Google Suggest, and Google Search History and argues that these three lesser-known Google tools warrant inclusion in the resourceful reference librarian’s bag of tricks.

  14. Fragrep: An Efficient Search Tool for Fragmented Patterns in Genomic Sequences

    Institute of Scientific and Technical Information of China (English)

    Axel Mosig; Katrin Sameith; Peter Stadler

    2006-01-01

    Many classes of non-coding RNAs (ncRNAs; including Y RNAs, vault RNAs,RNase P RNAs, and MRP RNAs, as well as a novel class recently discovered in Dictyostelium discoideum) can be characterized by a pattern of short but wellconserved sequence elements that are separated by poorly conserved regions of sometimes highly variable lengths. Local alignment algorithms such as BLAST are therefore ill-suited for the discovery of new homologs of such ncRNAs in genomic sequences. The Fragrep tool instead implements an efficient algorithm for detecting the pattern fragments that occur in a given order. For each pattern fragment,the mismatch tolerance and bounds on the length of the intervening sequences can be specified separately. Furthermore, matches can be ranked by a statistically well-motivated scoring scheme.

  15. Pin-Align: A New Dynamic Programming Approach to Align Protein-Protein Interaction Networks

    OpenAIRE

    Farid Amir-Ghiasvand; Abbas Nowzari-Dalini; Vida Momenzadeh

    2014-01-01

    To date, few tools for aligning protein-protein interaction networks have been suggested. These tools typically find conserved interaction patterns using various local or global alignment algorithms. However, the improvement of the speed, scalability, simplification, and accuracy of network alignment tools is still the target of new researches. In this paper, we introduce Pin-Align, a new tool for local alignment of protein-protein interaction networks. Pin-Align accuracy is tested on protein...

  16. SearchLight: a freely available web-based quantitative spectral analysis tool (Conference Presentation)

    Science.gov (United States)

    Prabhat, Prashant; Peet, Michael; Erdogan, Turan

    2016-03-01

    In order to design a fluorescence experiment, typically the spectra of a fluorophore and of a filter set are overlaid on a single graph and the spectral overlap is evaluated intuitively. However, in a typical fluorescence imaging system the fluorophores and optical filters are not the only wavelength dependent variables - even the excitation light sources have been changing. For example, LED Light Engines may have a significantly different spectral response compared to the traditional metal-halide lamps. Therefore, for a more accurate assessment of fluorophore-to-filter-set compatibility, all sources of spectral variation should be taken into account simultaneously. Additionally, intuitive or qualitative evaluation of many spectra does not necessarily provide a realistic assessment of the system performance. "SearchLight" is a freely available web-based spectral plotting and analysis tool that can be used to address the need for accurate, quantitative spectral evaluation of fluorescence measurement systems. This tool is available at: http://searchlight.semrock.com/. Based on a detailed mathematical framework [1], SearchLight calculates signal, noise, and signal-to-noise ratio for multiple combinations of fluorophores, filter sets, light sources and detectors. SearchLight allows for qualitative and quantitative evaluation of the compatibility of filter sets with fluorophores, analysis of bleed-through, identification of optimized spectral edge locations for a set of filters under specific experimental conditions, and guidance regarding labeling protocols in multiplexing imaging assays. Entire SearchLight sessions can be shared with colleagues and collaborators and saved for future reference. [1] Anderson, N., Prabhat, P. and Erdogan, T., Spectral Modeling in Fluorescence Microscopy, http://www.semrock.com (2010).

  17. Search for anisotropic light propagation as a function of laser beam alignment relative to the Earth's velocity vector

    OpenAIRE

    Navia C. E.; Augusto C. R. A.; Franceschini D. F.; Robba M. B.; Tsui K. H.,

    2006-01-01

    A laser diffraction experiment was conducted to study light propagation in air. The experiment is easy to reproduce and it is based on simple optical principles. Two optical sensors (segmented photo-diodes) are used for measuring the position of diffracted light spots with a precision better than 0.1 μ m. The goal is to look for signals of anisotropic light propagation as function of the laser beam alignment to the Earth’s motion (solar barycenter motion) obtain...

  18. Data Albums: An Event Driven Search, Aggregation and Curation Tool for Earth Science

    Science.gov (United States)

    Ramachandran, Rahul; Kulkarni, Ajinkya; Maskey, Manil; Bakare, Rohan; Basyal, Sabin; Li, Xiang; Flynn, Shannon

    2014-01-01

    One of the largest continuing challenges in any Earth science investigation is the discovery and access of useful science content from the increasingly large volumes of Earth science data and related information available. Approaches used in Earth science research such as case study analysis and climatology studies involve gathering discovering and gathering diverse data sets and information to support the research goals. Research based on case studies involves a detailed description of specific weather events using data from different sources, to characterize physical processes in play for a specific event. Climatology-based research tends to focus on the representativeness of a given event, by studying the characteristics and distribution of a large number of events. This allows researchers to generalize characteristics such as spatio-temporal distribution, intensity, annual cycle, duration, etc. To gather relevant data and information for case studies and climatology analysis is both tedious and time consuming. Current Earth science data systems are designed with the assumption that researchers access data primarily by instrument or geophysical parameter. Those who know exactly the datasets of interest can obtain the specific files they need using these systems. However, in cases where researchers are interested in studying a significant event, they have to manually assemble a variety of datasets relevant to it by searching the different distributed data systems. In these cases, a search process needs to be organized around the event rather than observing instruments. In addition, the existing data systems assume users have sufficient knowledge regarding the domain vocabulary to be able to effectively utilize their catalogs. These systems do not support new or interdisciplinary researchers who may be unfamiliar with the domain terminology. This paper presents a specialized search, aggregation and curation tool for Earth science to address these existing

  19. Fast statistical alignment.

    Directory of Open Access Journals (Sweden)

    Robert K Bradley

    2009-05-01

    Full Text Available We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment--previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches--yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/.

  20. Fast statistical alignment.

    Science.gov (United States)

    Bradley, Robert K; Roberts, Adam; Smoot, Michael; Juvekar, Sudeep; Do, Jaeyoung; Dewey, Colin; Holmes, Ian; Pachter, Lior

    2009-05-01

    We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multiple alignments which are accompanied by estimates of the alignment accuracy and uncertainty for every column and character of the alignment--previously available only with alignment programs which use computationally-expensive Markov Chain Monte Carlo approaches--yet can align thousands of long sequences. Moreover, FSA utilizes an unsupervised query-specific learning procedure for parameter estimation which leads to improved accuracy on benchmark reference alignments in comparison to existing programs. The centroid alignment approach taken by FSA, in combination with its learning procedure, drastically reduces the amount of false-positive alignment on biological data in comparison to that given by other methods. The FSA program and a companion visualization tool for exploring uncertainty in alignments can be used via a web interface at http://orangutan.math.berkeley.edu/fsa/, and the source code is available at http://fsa.sourceforge.net/. PMID:19478997

  1. In search of the true universe the tools, shaping, and cost of cosmological thought

    CERN Document Server

    Harwit, Martin

    2013-01-01

    Astrophysicist and scholar Martin Harwit examines how our understanding of the cosmos advanced rapidly during the twentieth century and identifies the factors contributing to this progress. Astronomy, whose tools were largely imported from physics and engineering, benefited mid-century from the US policy of coupling basic research with practical national priorities. This strategy, initially developed for military and industrial purposes, provided astronomy with powerful tools yielding access - at virtually no cost - to radio, infrared, X-ray, and gamma-ray observations. Today, astronomers are investigating the new frontiers of dark matter and dark energy, critical to understanding the cosmos but of indeterminate socio-economic promise. Harwit addresses these current challenges in view of competing national priorities and proposes alternative new approaches in search of the true Universe. This is an engaging read for astrophysicists, policy makers, historians, and sociologists of science looking to learn and a...

  2. Genomic multiple sequence alignments: refinement using a genetic algorithm

    Directory of Open Access Journals (Sweden)

    Lefkowitz Elliot J

    2005-08-01

    Full Text Available Abstract Background Genomic sequence data cannot be fully appreciated in isolation. Comparative genomics – the practice of comparing genomic sequences from different species – plays an increasingly important role in understanding the genotypic differences between species that result in phenotypic differences as well as in revealing patterns of evolutionary relationships. One of the major challenges in comparative genomics is producing a high-quality alignment between two or more related genomic sequences. In recent years, a number of tools have been developed for aligning large genomic sequences. Most utilize heuristic strategies to identify a series of strong sequence similarities, which are then used as anchors to align the regions between the anchor points. The resulting alignment is globally correct, but in many cases is suboptimal locally. We describe a new program, GenAlignRefine, which improves the overall quality of global multiple alignments by using a genetic algorithm to improve local regions of alignment. Regions of low quality are identified, realigned using the program T-Coffee, and then refined using a genetic algorithm. Because a better COFFEE (Consistency based Objective Function For alignmEnt Evaluation score generally reflects greater alignment quality, the algorithm searches for an alignment that yields a better COFFEE score. To improve the intrinsic slowness of the genetic algorithm, GenAlignRefine was implemented as a parallel, cluster-based program. Results We tested the GenAlignRefine algorithm by running it on a Linux cluster to refine sequences from a simulation, as well as refine a multiple alignment of 15 Orthopoxvirus genomic sequences approximately 260,000 nucleotides in length that initially had been aligned by Multi-LAGAN. It took approximately 150 minutes for a 40-processor Linux cluster to optimize some 200 fuzzy (poorly aligned regions of the orthopoxvirus alignment. Overall sequence identity increased only

  3. Developing a Search Algorithm and a Visualization Tool for SNOMED CT

    Directory of Open Access Journals (Sweden)

    Anthony Masi

    2015-04-01

    Full Text Available With electronic health records rising in popularity among hospitals and physicians, the SNOMED CT medical terminology has served as a valuable standard for those looking to exchange a variety of information linked to clinical knowledge bases, information retrieval, and data aggregation. However, SNOMED CT is distributed as a flat file database by the International Health Terminology Standards Development Organization and visualization of data can be a problem. This study describes an algorithm that allows a user to easily search SNOMED CT for identical or partial matches utilizing indexing and wildcard matching through a graphical user interface developed in the cross-platform programming language Java. In addition to this, the algorithm displays corresponding relationships and other relevant information pertaining to the search term. The outcome of this study can serve as a useful visualization tool for those looking to delve into the increasingly standardized world of electronic health records as well as a tool for healthcare providers who may be seeking specific clinical information contained in the SNOMED CT database.

  4. PALM-IST: Pathway Assembly from Literature Mining--an Information Search Tool.

    Science.gov (United States)

    Mandloi, Sapan; Chakrabarti, Saikat

    2015-01-01

    Manual curation of biomedical literature has become extremely tedious process due to its exponential growth in recent years. To extract meaningful information from such large and unstructured text, newer and more efficient mining tool is required. Here, we introduce PALM-IST, a computational platform that not only allows users to explore biomedical abstracts using keyword based text mining but also extracts biological entity (e.g., gene/protein, drug, disease, biological processes, cellular component, etc.) information from the extracted text and subsequently mines various databases to provide their comprehensive inter-relation (e.g., interaction, expression, etc.). PALM-IST constructs protein interaction network and pathway information data relevant to the text search using multiple data mining tools and assembles them to create a meta-interaction network. It also analyzes scientific collaboration by extraction and creation of "co-authorship network," for a given search context. Hence, this useful combination of literature and data mining provided in PALM-IST can be used to extract novel protein-protein interaction (PPI), to generate meta-pathways and further to identify key crosstalk and bottleneck proteins. PALM-IST is available at www.hpppi.iicb.res.in/ctm. PMID:25989388

  5. The NERIES Data Portal : building a distributed heterogeneous data search, access, and processing tool set

    Science.gov (United States)

    Kamb, Linus; Spinuso, Alessandro; Frobert, Laurent; Trani, Luca; Bossu, Remy; van Eck, Torild

    2010-05-01

    The NERIES project (NEtwork of Research Infrastructures for European Seismology) is an EC-funded Integrated Infrastructure Initiative (I3) under the 6th Framework Programme developed to integrate data and service resources for the seismological community. The NERIES data portal (http://www.seismicportal.eu) provides a single integrated point of access to distributed data sets available from several of the NERIES activities. The data portal aggregates data search and access tools from several NERIES participants within a unified access point. These tools operate in a coordinated manner to provide a cohesive distributed search environment, linking data search and access across multiple data providers. In addition, the portal provides a platform from which to integrate access to external tools and processing centers. The NERIES data portal is architected as a collection of JSR-168-compliant web portlets operating at the respective data centers, and supported by a distributed collection of web services. The portlets access both local and remote web data services. The data services are exposed through standard HTTP access mechanisms and are thus available for direct access by other external clients. This allows the creation of independent applications that access the data center holdings directly through these exposed web data services. The nature of the portlet standard allows the NERIES portlets to be included, using remote portlet technologies, in outside portal efforts, offering an opportunity to leverage and reuse existing tools. Ongoing efforts will continue to build on the successes and building-blocks of the NERIES project to further develop an integrated data access model to provide a foundation on which to build access to external processing resources and data utilities, and to broaden the range of data sets accessible through the portal. With an integrated data access model, a data workbench is built in which users can define custom personalized data sets

  6. Mutagenesis Objective Search and Selection Tool (MOSST: an algorithm to predict structure-function related mutations in proteins

    Directory of Open Access Journals (Sweden)

    Asenjo Juan A

    2011-04-01

    Full Text Available Abstract Background Functionally relevant artificial or natural mutations are difficult to assess or predict if no structure-function information is available for a protein. This is especially important to correctly identify functionally significant non-synonymous single nucleotide polymorphisms (nsSNPs or to design a site-directed mutagenesis strategy for a target protein. A new and powerful methodology is proposed to guide these two decision strategies, based only on conservation rules of physicochemical properties of amino acids extracted from a multiple alignment of a protein family where the target protein belongs, with no need of explicit structure-function relationships. Results A statistical analysis is performed over each amino acid position in the multiple protein alignment, based on different amino acid physical or chemical characteristics, including hydrophobicity, side-chain volume, charge and protein conformational parameters. The variances of each of these properties at each position are combined to obtain a global statistical indicator of the conservation degree of each property. Different types of physicochemical conservation are defined to characterize relevant and irrelevant positions. The differences between statistical variances are taken together as the basis of hypothesis tests at each position to search for functionally significant mutable sites and to identify specific mutagenesis targets. The outcome is used to statistically predict physicochemical consensus sequences based on different properties and to calculate the amino acid propensities at each position in a given protein. Hence, amino acid positions are identified that are putatively responsible for function, specificity, stability or binding interactions in a family of proteins. Once these key functional positions are identified, position-specific statistical distributions are applied to divide the 20 common protein amino acids in each position of the protein

  7. metAlignID: A high-throughout sofware tool set for automated detection of trace level contaminants in comprehensive LECO two-dimensional gas chromatography time-of-flight mass spectrometry data

    NARCIS (Netherlands)

    Lommen, A.; Kamp, van der H.J.; Kools, H.J.; Lee, van der M.K.; Weg, van der G.

    2012-01-01

    A new alternative data processing tool set, metAlignID, is developed for automated pre-processing and library-based identification and concentration estimation of target compounds after analysis by comprehensive two-dimensional gas chromatography with mass spectrometric detection. The tool set has b

  8. ANDY: A general, fault-tolerant tool for database searching oncomputer clusters

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Andrew; Chandonia, John-Marc; Brenner, Steven E.

    2005-12-21

    Summary: ANDY (seArch coordination aND analYsis) is a set ofPerl programs and modules for distributing large biological databasesearches, and in general any sequence of commands, across the nodes of aLinux computer cluster. ANDY is compatible with several commonly usedDistributed Resource Management (DRM) systems, and it can be easilyextended to new DRMs. A distinctive feature of ANDY is the choice ofeither dedicated or fair-use operation: ANDY is almost as efficient assingle-purpose tools that require a dedicated cluster, but it runs on ageneral-purpose cluster along with any other jobs scheduled by a DRM.Other features include communication through named pipes for performance,flexible customizable routines for error-checking and summarizingresults, and multiple fault-tolerance mechanisms. Availability: ANDY isfreely available and may be obtained fromhttp://compbio.berkeley.edu/proj/andy; this site also containssupplemental data and figures and amore detailed overview of thesoftware.

  9. Simple tool to search quasi-magic structures in deformed nuclei

    International Nuclear Information System (INIS)

    Strutinsky method the smooth energy of the nucleus is obtained by a folding procedure of the single-particle (s.p.) energy density in the s.p. energy space e. An alternative way of energy smoothing is obtained by folding the s.p. energy sum in the particle-number space N. For non degenerated s.p. spectra both types of folding yield smooth energies which are close to each other. In the case of strongly degenerated spectra which appear at sphericity or in regions of shape isomers, the smooth energy obtained by the N-folding is a couple of MeV larger than the traditional average Strutinsky energy. It is shown that this smooth energy difference can serve as a simple tool to search for magic or quasi-magic structures in the s.p. spectra, e.g. to find shape isomers in the multidimensional deformation space. (author)

  10. SPLICER - A GENETIC ALGORITHM TOOL FOR SEARCH AND OPTIMIZATION, VERSION 1.0 (MACINTOSH VERSION)

    Science.gov (United States)

    Wang, L.

    1994-01-01

    SPLICER is a genetic algorithm tool which can be used to solve search and optimization problems. Genetic algorithms are adaptive search procedures (i.e. problem solving methods) based loosely on the processes of natural selection and Darwinian "survival of the fittest." SPLICER provides the underlying framework and structure for building a genetic algorithm application. These algorithms apply genetically-inspired operators to populations of potential solutions in an iterative fashion, creating new populations while searching for an optimal or near-optimal solution to the problem at hand. SPLICER 1.0 was created using a modular architecture that includes a Genetic Algorithm Kernel, interchangeable Representation Libraries, Fitness Modules and User Interface Libraries, and well-defined interfaces between these components. The architecture supports portability, flexibility, and extensibility. SPLICER comes with all source code and several examples. For instance, a "traveling salesperson" example searches for the minimum distance through a number of cities visiting each city only once. Stand-alone SPLICER applications can be used without any programming knowledge. However, to fully utilize SPLICER within new problem domains, familiarity with C language programming is essential. SPLICER's genetic algorithm (GA) kernel was developed independent of representation (i.e. problem encoding), fitness function or user interface type. The GA kernel comprises all functions necessary for the manipulation of populations. These functions include the creation of populations and population members, the iterative population model, fitness scaling, parent selection and sampling, and the generation of population statistics. In addition, miscellaneous functions are included in the kernel (e.g., random number generators). Different problem-encoding schemes and functions are defined and stored in interchangeable representation libraries. This allows the GA kernel to be used with any

  11. A search for new hot subdwarf stars by means of Virtual Observatory tools

    CERN Document Server

    Oreiro, R; Solano, E; Ulla, A; \\Ostensen, R; García-Torres, M

    2011-01-01

    Hot subdwarf stars are faint, blue objects, and are the main contributors to the far-UV excess observed in elliptical galaxies. They offer an excellent laboratory to study close and wide binary systems, and to scrutinize their interiors through asteroseismology, as some of them undergo stellar oscillations. However, their origins are still uncertain, and increasing the number of detections is crucial to undertake statistical studies. In this work, we aim at defining a strategy to find new, uncatalogued hot subdwarfs. Making use of Virtual Observatory tools we thoroughly search stellar catalogues to retrieve multi-colour photometry and astrometric information of a known sample of blue objects, including hot subdwarfs, white dwarfs, cataclysmic variables and main sequence OB stars. We define a procedure to discriminate among these spectral classes, particularly designed to obtain a hot subdwarf sample with a low contamination factor. In order to check the validity of the method, this procedure is then applied t...

  12. IPeak: An open source tool to combine results from multiple MS/MS search engines.

    Science.gov (United States)

    Wen, Bo; Du, Chaoqin; Li, Guilin; Ghali, Fawaz; Jones, Andrew R; Käll, Lukas; Xu, Shaohang; Zhou, Ruo; Ren, Zhe; Feng, Qiang; Xu, Xun; Wang, Jun

    2015-09-01

    Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present an open source software tool, termed IPeak, a peptide identification pipeline that is designed to combine the Percolator post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak provides a graphical user interface (GUI) as well as a command-line interface, which is implemented in JAVA and can work on all three major operating system platforms: Windows, Linux/Unix and OS X. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard. IPeak is freely available and can be downloaded under an Apache 2.0 license at https://code.google.com/p/mzidentml-lib/. PMID:25951428

  13. The Search for Astronomical Alignments in the Seventh Century A.D. Silla Capital at Kyongju, Korea

    Science.gov (United States)

    Nelson, S. M.; Stencel, R. E.

    1999-05-01

    In the center of the modern Korean city of Kyongju stands a modest structure dating from the 7th century AD, known as Chomsongdae, or the Star Observatory. Known locally as the oldest observatory in Asia, details of its precise use are lost, but its construction coincided with the height of Silla culture and its dominance over the Korean peninsula. Radially from the structure are located the so-called Moon Fortress, numerous large tombsites for elite of the culture, plus hillside fortresses and elaborate Buddhist temples. During 1999, we've conducted a course at Denver as part of our Core Curriculum program for The Women's College, that has examined the astronomical and cultural aspects of the Kyongju site, to attempt to determine whether the architects may have included astronomical alignments into the ``Feng Shui" of their city planning, spanning centuries. The preliminary result of our studies suggests that east and west of Star Observatory lay fortress and wall features that may have been useful for equinox determination. A discussion of ethnographic supporting evidence will be provided, but additional on-site observations will be needed to confirm the idea.

  14. Neuron-Miner: An Advanced Tool for Morphological Search and Retrieval in Neuroscientific Image Databases.

    Science.gov (United States)

    Conjeti, Sailesh; Mesbah, Sepideh; Negahdar, Mohammadreza; Rautenberg, Philipp L; Zhang, Shaoting; Navab, Nassir; Katouzian, Amin

    2016-10-01

    The steadily growing amounts of digital neuroscientific data demands for a reliable, systematic, and computationally effective retrieval algorithm. In this paper, we present Neuron-Miner, which is a tool for fast and accurate reference-based retrieval within neuron image databases. The proposed algorithm is established upon hashing (search and retrieval) technique by employing multiple unsupervised random trees, collectively called as Hashing Forests (HF). The HF are trained to parse the neuromorphological space hierarchically and preserve the inherent neuron neighborhoods while encoding with compact binary codewords. We further introduce the inverse-coding formulation within HF to effectively mitigate pairwise neuron similarity comparisons, thus allowing scalability to massive databases with little additional time overhead. The proposed hashing tool has superior approximation of the true neuromorphological neighborhood with better retrieval and ranking performance in comparison to existing generalized hashing methods. This is exhaustively validated by quantifying the results over 31266 neuron reconstructions from Neuromorpho.org dataset curated from 147 different archives. We envisage that finding and ranking similar neurons through reference-based querying via Neuron Miner would assist neuroscientists in objectively understanding the relationship between neuronal structure and function for applications in comparative anatomy or diagnosis. PMID:27155864

  15. Novel DOCK clique driven 3D similarity database search tools for molecule shape matching and beyond: adding flexibility to the search for ligand kin.

    Science.gov (United States)

    Good, Andrew C

    2007-10-01

    With readily available CPU power and copious disk storage, it is now possible to undertake rapid comparison of 3D properties derived from explicit ligand overlay experiments. With this in mind, shape software tools originally devised in the 1990s are revisited, modified and applied to the problem of ligand database shape comparison. The utility of Connolly surface data is highlighted using the program MAKESITE, which leverages surface normal data to a create ligand shape cast. This cast is applied directly within DOCK, allowing the program to be used unmodified as a shape searching tool. In addition, DOCK has undergone multiple modifications to create a dedicated ligand shape comparison tool KIN. Scoring has been altered to incorporate the original incarnation of Gaussian function derived shape description based on STO-3G atomic electron density. In addition, a tabu-like search refinement has been added to increase search speed by removing redundant starting orientations produced during clique matching. The ability to use exclusion regions, again based on Gaussian shape overlap, has also been integrated into the scoring function. The use of both DOCK with MAKESITE and KIN in database screening mode is illustrated using a published ligand shape virtual screening template. The advantages of using a clique-driven search paradigm are highlighted, including shape optimization within a pharmacophore constrained framework, and easy incorporation of additional scoring function modifications. The potential for further development of such methods is also discussed. PMID:17482856

  16. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  17. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  18. MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs

    Directory of Open Access Journals (Sweden)

    Tsunoda Tatsuhiko

    2007-03-01

    Full Text Available Abstract Background A combination of multiple types of transcription factors and cis-regulatory elements is often required for gene expression in eukaryotes, and the combinatorial regulation confers specific gene expression to tissues or environments. To reveal the combinatorial regulation, computational methods are developed that efficiently infer combinations of cis-regulatory motifs that are important for gene expression as measured by DNA microarrays. One promising type of computational method is to utilize regression analysis between expression levels and scores of motifs in input sequences. This type takes full advantage of information on expression levels because it does not require that the expression level of each gene be dichotomized according to whether or not it reaches a certain threshold level. However, there is no web-based tool that employs regression methods to systematically search for motif combinations and that practically handles combinations of more than two or three motifs. Results We here introduced MotifCombinator, an online tool with a user-friendly interface, to systematically search for combinations composed of any number of motifs based on regression methods. The tool utilizes well-known regression methods (the multivariate linear regression, the multivariate adaptive regression spline or MARS, and the multivariate logistic regression method for this purpose, and uses the genetic algorithm to search for combinations composed of any desired number of motifs. The visualization systems in this tool help users to intuitively grasp the process of the combination search, and the backup system allows users to easily stop and restart calculations that are expected to require large computational time. This tool also provides preparatory steps needed for systematic combination search – i.e., selecting single motifs to constitute combinations and cutting out redundant similar motifs based on clustering analysis. Conclusion

  19. Search for Supersymmetry in Trilepton Final States with the ATLAS Detector and the Alignment of the ATLAS Silicon Tracker

    CERN Document Server

    Brandt, Oleg; Barr, A J

    2009-01-01

    One of the main goals of the ATLAS detector at the Large Hadron Collider of CERN, a proton-proton collider with a nominal centre-of-mass energy of 14 TeV, is to search for New Physics beyond the Standard Model. A widely favoured Beyond the Standard Model candidate is Supersymmetry (SUSY), which postulates a superpartner with the same quantum numbers, but a spin changed by 1/2 for each Standard Model particle. The first part of this thesis describes a strategy for an early discovery of SUSY using the trilepton signature, with a focus on gravity-mediated SUSY breaking, mSUGRA. The discovery potential for SUSY at the LHC for the case where strongly interacting supersymmetric particles are very massive is critically investigated. A possible choice of triggers for L = 10-31 cm-2 s-1 is suggested by optimising the event yield at intermediate and final selection stages. A novel method to measure the rate of leptons from heavy flavour decays passing isolation requirements by isolating tt events in data is outlined. T...

  20. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2011-01-01

    A new set of muon alignment constants was approved in August. The relative position between muon chambers is essentially unchanged, indicating good detector stability. The main changes concern the global positioning of the barrel and of the endcap rings to match the new Tracker geometry. Detailed studies of the differences between track-based and optical alignment of DTs have proven to be a valuable tool for constraining Tracker alignment weak modes, and this information is now being used as part of the alignment procedure. In addition to the “split-cosmic” analysis used to investigate the muon momentum resolution at high momentum, a new procedure based on reconstructing the invariant mass of di-muons from boosted Zs is under development. Both procedures show an improvement in the momentum precision of Global Muons with respect to Tracker-only Muons. Recent developments in track-based alignment include a better treatment of the tails of residual distributions and accounting for correla...

  1. PHASTER: a better, faster version of the PHAST phage search tool.

    Science.gov (United States)

    Arndt, David; Grant, Jason R; Marcu, Ana; Sajed, Tanvir; Pon, Allison; Liang, Yongjie; Wishart, David S

    2016-07-01

    PHASTER (PHAge Search Tool - Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. In particular, PHASTER is now 4.3× faster than PHAST when analyzing a typical bacterial genome. More specifically, software optimizations have made the backend of PHASTER 2.7X faster than PHAST, while the addition of 80 CPUs to the PHASTER compute cluster are responsible for the remaining speed-up. PHASTER can now process a typical bacterial genome in 3 min from the raw sequence alone, or in 1.5 min when given a pre-annotated GenBank file. A number of other optimizations have also been implemented, including automated algorithms to reduce the size and redundancy of PHASTER's databases, improvements in handling multiple (metagenomic) queries and higher user traffic, along with the ability to perform automated look-ups against 14 000 previously PHAST/PHASTER annotated bacterial genomes (which can lead to complete phage annotations in seconds as opposed to minutes). PHASTER's web interface has also been entirely rewritten. A new graphical genome browser has been added, gene/genome visualization tools have been improved, and the graphical interface is now more modern, robust and user-friendly. PHASTER is available online at www.phaster.ca. PMID:27141966

  2. FANSe2: a robust and cost-efficient alignment tool for quantitative next-generation sequencing applications.

    Directory of Open Access Journals (Sweden)

    Chuan-Le Xiao

    Full Text Available Correct and bias-free interpretation of the deep sequencing data is inevitably dependent on the complete mapping of all mappable reads to the reference sequence, especially for quantitative RNA-seq applications. Seed-based algorithms are generally slow but robust, while Burrows-Wheeler Transform (BWT based algorithms are fast but less robust. To have both advantages, we developed an algorithm FANSe2 with iterative mapping strategy based on the statistics of real-world sequencing error distribution to substantially accelerate the mapping without compromising the accuracy. Its sensitivity and accuracy are higher than the BWT-based algorithms in the tests using both prokaryotic and eukaryotic sequencing datasets. The gene identification results of FANSe2 is experimentally validated, while the previous algorithms have false positives and false negatives. FANSe2 showed remarkably better consistency to the microarray than most other algorithms in terms of gene expression quantifications. We implemented a scalable and almost maintenance-free parallelization method that can utilize the computational power of multiple office computers, a novel feature not present in any other mainstream algorithm. With three normal office computers, we demonstrated that FANSe2 mapped an RNA-seq dataset generated from an entire Illunima HiSeq 2000 flowcell (8 lanes, 608 M reads to masked human genome within 4.1 hours with higher sensitivity than Bowtie/Bowtie2. FANSe2 thus provides robust accuracy, full indel sensitivity, fast speed, versatile compatibility and economical computational utilization, making it a useful and practical tool for deep sequencing applications. FANSe2 is freely available at http://bioinformatics.jnu.edu.cn/software/fanse2/.

  3. A 'tubeless' Portable Radiation Search Tool (PRST) for special nuclear materials

    International Nuclear Information System (INIS)

    Nuclear Safeguards and Security Systems LLC (NucSafe) has produced a briefcase packaged Portable Radiation Search Tool (PRST) for the IAEA Safeguards Group. The PRST detects Special Nuclear Materials (SNM) by measuring neutrons and gamma rays. Neutron sensors are comprised of scintillating glass fibers, which provide several advantages over conventional 3He and 10BF3 tubes. These 6Li glass fiber sensors offer higher neutron sensitivity, increased dynamic counting range, eliminate transport and operational hazards, and have significantly less microphonic susceptibility than gas tubes. Bismuth Germanate (BGO) is used as the gamma detector due to its higher intrinsic efficiency relative to Sodium Iodide (NalTI) detectors. Since gamma spectrometry senso stricto is not a system requirement, gross gamma counting in six regions of interest was designed for the PRST search functions. The system must be as light as possible and is now ∼8 kg with an overall size of 46x36x15 cm. The unit uses smart lithium ion batteries that may be exchanged with a fresh pack or recharged during operation. Operating time with fully charged batteries is 8 to 10 hours. The PRST does not require an external computer for operation. Onboard electronics allows the system to integrate data over multiple counting times and provides over-sampling and peak detection and hold for short alarm events. Users can independently adjust a number of parameters including set points for neutron and gamma channel alarms, but system operation is very simple. PRST neutron sensors contain 5 layers of glass fiber ribbons vice the 3-layer glass fiber panels used in NucSafe SNM monitors for vehicles, portals, and freight. Five layers provide the additional sensitivity needed since detector areas are limited by portability requirements for the PRST Monte Carlo (MCNP) modeling has demonstrated that moderation is more important thai detector active area in attaining the highest intrinsic efficiency for a given mass of

  4. The Canadian light source: A novel tool in the search for environmental sustainability

    International Nuclear Information System (INIS)

    As applied research moves into the 21st century, industry is discovering that traditional analytical techniques are not answering all of their questions. For example, new materials are being developed daily that may have significantly different properties but are chemically indistinguishable using current analysis techniques. It is important for industry to understand these differences and be able to go back to the laboratory and impart those unique properties to a new product. Therefore, today, industry is turning to new tools to shed light on old and new questions. In a similar manner, environmental waste management is motivating many proactive industries to move toward new technologies that will provide answers to environmental questions yet to be asked. Within the mining sector, the ability to understand and predict the long-term stability and future bioavailability of metals (e.g., arsenic) in mine waste is critical for operation and absolutely essential to their capacity to decommission that site in the future. Currently, the environmental impact of tailings is monitored and stability is predicted by combining thermodynamic models with powder x-ray diffraction data to determine material composition and with assorted wet chemistry techniques to determine total species concentrations. Although these techniques have supplied a significant amount of important ecological information, increasing pressure from environmental groups demand more detailed information beyond the range of these procedures. To obtain this increasing level of detail, scientist are turning to more sophisticated analytical tools such as such as synchrotron radiation-based x-ray absorption spectroscopy (XAS) for insight. XAS is a powerful probe that can directly determine the oxidation states and local chemical surroundings of a metal and thereby increase our understanding of its long term environmental impact. With environmental stewardship being of global concern, the Canadian Light Source

  5. Google's incentive for entrepreneurs: internet tools for Search Engine Optimization and online advertising

    OpenAIRE

    Rovesti, Luca

    2012-01-01

    The goal of the thesis is to assess the effectiveness of Search Engine Optimization on E-commerce for small companies. A case of study method was chosen: the Search Engine Optimization approaches presented in the review of theory were tested at the Rovesti Technologies Company. The review of theory exposes online advertising and Search Engine Optimization’s characteristics and strategies, with particular focus on Return on Investment. Relevant material for this thesis had been collected ...

  6. The CHRONIOUS Ontology-Driven Search Tool: Enabling Access to Focused and Up-to-Date Healthcare Literature

    CERN Document Server

    Kiefer, Stephan; Albertoni, Riccardo; Attene, Marco; Giannini, Franca; Marini, Simone; Schneider, Luc; Mesquita, Carlos; Xing, Xin; Lawo, Michael

    2011-01-01

    This paper presents an advanced search engine prototype for bibliography retrieval developed within the CHRONIOUS European IP project of the seventh Framework Program (FP7). This search engine is specifically targeted to clinicians and healthcare practitioners searching for documents related to Chronic Obstructive Pulmonary Disease (COPD) and Chronic Kidney Disease (CKD). To this aim, the presented tool exploits two pathology-specific ontologies that allow focused document indexing and retrieval. These ontologies have been developed on the top of the Middle Layer Ontology for Clinical Care (MLOCC), which provides a link with the Basic Formal Ontology, a foundational ontology used in the Open Biological and Biomedical Ontologies (OBO) Foundry. In addition link with the terms of the MeSH (Medical Subject Heading) thesaurus has been provided to guarantee the coverage with the general certified medical terms and multilingual capabilities.

  7. Alignment validation

    CERN Document Server

    Golling, T

    2007-01-01

    The four experiments, ALICE, ATLAS, CMS and LHCb are currently under construction at CERN. They will study the products of proton-proton collisions at the Large Hadron Collider. All experiments are equipped with sophisticated tracking systems, unprecedented in size and complexity. Full exploitation of both the inner detector and the muon system requires an accurate alignment of all detector elements. Alignment information is deduced from dedicated hardware alignment systems and the reconstruction of charged particles. However, the system is degenerate which means the data is insufficient to constrain all alignment degrees of freedom, so the techniques are prone to converging on wrong geometries. This deficiency necessitates validation and monitoring of the alignment. An exhaustive discussion of means to validate is subject to this document, including examples and plans from all four LHC experiments, as well as other high energy experiments.

  8. Diverse sequence search and alignment

    OpenAIRE

    Eser, Elif

    2013-01-01

    Ankara : The Department of Computer Engineering and the Graduate School of Engineering and Science of Bilkent University, 2013. Thesis (Master's) -- Bilkent University, 2013. Includes bibliographical references leaves 51-54. Eser, Elif Master's

  9. The Signal Data Explorer: A high performance Grid based signal search tool for use in distributed diagnostic applications

    OpenAIRE

    Fletcher, Martyn; Jackson, Tom; Jessop, Mark; Liang, Bojian; Austin, Jim

    2006-01-01

    We describe a high performance Grid based signal search tool for distributed diagnostic applications developed in conjunction with Rolls-Royce plc for civil aero engine condition monitoring applications. With the introduction of advanced monitoring technology into engineering systems, healthcare, etc., the associated diagnostic processes are increasingly required to handle and consider vast amounts of data. An exemplar of such a diagnosis process was developed during the DAME project, which b...

  10. 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].

  11. Tracing Translation Universals and Translator Development by Word Aligning a Harry Potter Corpus

    OpenAIRE

    Helgegren, Sofia

    2005-01-01

    For the purpose of this descriptive translation study, a translation corpus was built from roughly the first 20,000 words of each of the first four Harry Potter books by J.K. Rowling, and their respective translations into Swedish. I*Link, a new type of word alignment tool, was used to align the samples on a word level and to investigate and analyse the aligned corpus. The purpose of the study was threefold: to investigate manifestations of translation universals, to search for evidence of tr...

  12. Hardware Accelerated Sequence Alignment with Traceback

    OpenAIRE

    Scott Lloyd; Snell, Quinn O

    2009-01-01

    Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is pres...

  13. Diboson search and multivariate tools in the pp→ιν + heavy flavor channel at CDF

    International Nuclear Information System (INIS)

    This paper describes the application of machine learning techniques to the diboson search in the lepton plus neutrino plus heavy flavor jets channel at CDF. Three different aspects of this challenging search are analyzed: multijet background rejection with the use of a support vector machine discriminant, light/heavy flavor jets separation with a 26 input variable neural network and b-jet specific energy corrections, where a resolution improvement is obtained feeding a neural network with both calorimeter and tracking information.

  14. search.bioPreprint: a discovery tool for cutting edge, preprint biomedical research articles [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Carrie L. Iwema

    2016-07-01

    Full Text Available The time it takes for a completed manuscript to be published traditionally can be extremely lengthy. Article publication delay, which occurs in part due to constraints associated with peer review, can prevent the timely dissemination of critical and actionable data associated with new information on rare diseases or developing health concerns such as Zika virus. Preprint servers are open access online repositories housing preprint research articles that enable authors (1 to make their research immediately and freely available and (2 to receive commentary and peer review prior to journal submission. There is a growing movement of preprint advocates aiming to change the current journal publication and peer review system, proposing that preprints catalyze biomedical discovery, support career advancement, and improve scientific communication. While the number of articles submitted to and hosted by preprint servers are gradually increasing, there has been no simple way to identify biomedical research published in a preprint format, as they are not typically indexed and are only discoverable by directly searching the specific preprint server websites. To address this issue, we created a search engine that quickly compiles preprints from disparate host repositories and provides a one-stop search solution. Additionally, we developed a web application that bolsters the discovery of preprints by enabling each and every word or phrase appearing on any web site to be integrated with articles from preprint servers. This tool, search.bioPreprint, is publicly available at http://www.hsls.pitt.edu/resources/preprint.

  15. Project GRACE A grid based search tool for the global digital library

    CERN Document Server

    Scholze, Frank; Vigen, Jens; Prazak, Petra; The Seventh International Conference on Electronic Theses and Dissertations

    2004-01-01

    The paper will report on the progress of an ongoing EU project called GRACE - Grid Search and Categorization Engine (http://www.grace-ist.org). The project participants are CERN, Sheffield Hallam University, Stockholm University, Stuttgart University, GL 2006 and Telecom Italia. The project started in 2002 and will finish in 2005, resulting in a Grid based search engine that will search across a variety of content sources including a number of electronic thesis and dissertation repositories. The Open Archives Initiative (OAI) is expanding and is clearly an interesting movement for a community advocating open access to ETD. However, the OAI approach alone may not be sufficiently scalable to achieve a truly global ETD Digital Library. Many universities simply offer their collections to the world via their local web services without being part of any federated system for archiving and even those dissertations that are provided with OAI compliant metadata will not necessarily be picked up by a centralized OAI Ser...

  16. Where Does the Alignment Score Distribution Shape Come from?

    Science.gov (United States)

    Ortet, Philippe; Bastien, Olivier

    2010-01-01

    Alignment algorithms are powerful tools for searching for homologous proteins in databases, providing a score for each sequence present in the database. It has been well known for 20 years that the shape of the score distribution looks like an extreme value distribution. The extremely large number of times biologists face this class of distributions raises the question of the evolutionary origin of this probability law. We investigated the possibility of deriving the main properties of sequence alignment score distributions from a basic evolutionary process: a duplication-divergence protein evolution process in a sequence space. Firstly, the distribution of sequences in this space was defined with respect to the genetic distance between sequences. Secondly, we derived a basic relation between the genetic distance and the alignment score. We obtained a novel score probability distribution which is qualitatively very similar to that of Karlin-Altschul but performing better than all other previous model. PMID:21258650

  17. Alignment of Custom Standards by Machine Learning Algorithms

    Directory of Open Access Journals (Sweden)

    Adela Sirbu

    2010-09-01

    Full Text Available Building an efficient model for automatic alignment of terminologies would bring a significant improvement to the information retrieval process. We have developed and compared two machine learning based algorithms whose aim is to align 2 custom standards built on a 3 level taxonomy, using kNN and SVM classifiers that work on a vector representation consisting of several similarity measures. The weights utilized by the kNN were optimized with an evolutionary algorithm, while the SVM classifier's hyper-parameters were optimized with a grid search algorithm. The database used for train was semi automatically obtained by using the Coma++ tool. The performance of our aligners is shown by the results obtained on the test set.

  18. Writing for the Robot: How Employer Search Tools Have Influenced Resume Rhetoric and Ethics

    Science.gov (United States)

    Amare, Nicole; Manning, Alan

    2009-01-01

    To date, business communication scholars and textbook writers have encouraged resume rhetoric that accommodates technology, for example, recommending keyword-enhancing techniques to attract the attention of searchbots: customized search engines that allow companies to automatically scan resumes for relevant keywords. However, few scholars have…

  19. Tools for model-independent bounds in direct dark matter searches

    CERN Document Server

    Del Nobile, Eugenio; Panci, Paolo

    2013-01-01

    We discuss a framework (based on non-relativistic operators) and a self-contained set of numerical tools to derive the bounds from some current direct detection experiments on any arbitrary model of Dark Matter.

  20. Tools for model-independent bounds in direct dark matter searches

    DEFF Research Database (Denmark)

    Cirelli, M.; Del Nobile, E.; Panci, P.

    2013-01-01

    We discuss a framework (based on non-relativistic operators) and a self-contained set of numerical tools to derive the bounds from some current direct detection experiments on virtually any arbitrary model of Dark Matter elastically scattering on nuclei.......We discuss a framework (based on non-relativistic operators) and a self-contained set of numerical tools to derive the bounds from some current direct detection experiments on virtually any arbitrary model of Dark Matter elastically scattering on nuclei....

  1. Beyond Alignment

    DEFF Research Database (Denmark)

    Beyond Alignment: Applying Systems Thinking to Architecting Enterprises is a comprehensive reader about how enterprises can apply systems thinking in their enterprise architecture practice, for business transformation and for strategic execution. The book's contributors find that systems thinking...... is a valuable way of thinking about the viable enterprise and how to architect it....

  2. Licensee event report sequence coding and search procedure: a training tool

    International Nuclear Information System (INIS)

    At the request of the Nuclear Regulatory Commission's Office for Analysis and Evaluation of Operational Data (AEOD), the Nuclear Safety Information Center (NSIC) has undertaken the development of a detailed computer-compatible coding system for events and sequences of occurrences described in Licensee Event Reports (LERs). This task was conceived by AEOD and is designated the LER Sequence Coding and Search Procedure. The coding system is intended to describe the sequence of events detailed in the LER in a computer-readable and computer-searchable format. The NSIC has developed coding tables, a coding form and compatible computer software to permit storage and on-line computer search capability. The AEOD draft Watch List has been revised to categorize and retrieve identified situations of interest. The coding system provides an orderly presentation of occurrences that resulted because of an initiating event. The sequences could be used for training operators and maintenance personnel in transients that have actually occurred

  3. EC-BLAST: A Tool to Automatically Search and Compare Enzyme Reactions

    OpenAIRE

    Rahman, Syed Asad; Cuesta, Sergio Martinez; Furnham, Nicholas; Holliday, Gemma L.; Thornton, Janet M

    2014-01-01

    EC-BLAST is an algorithm for quantitative similarity searches between enzyme reactions at three levels a) bond change, b) reaction centre and c) reaction structure similarity. It exploits the knowledge of bond changes and reaction patterns for all known biochemical reactions derived from atom-atom mapping (AAM) across each reaction. This has the potential to improve the established enzyme classification system, to find novel biochemical transformations, to improve the assignment of enzyme fun...

  4. Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy

    OpenAIRE

    2012-01-01

    Background NCRNAs (noncoding RNAs) play important roles in many biological processes. Existing genome-scale ncRNA search tools identify ncRNAs in local sequence alignments generated by conventional sequence comparison methods. However, some types of ncRNA lack strong sequence conservation and tend to be missed or mis-aligned by conventional sequence comparison. Results In this paper, we propose an ncRNA identification framework that is complementary to existing sequence comparison tools. By i...

  5. Searching for New Directions: Developing MA Action Research Project as a Tool for Teaching

    Science.gov (United States)

    Lee, Young Ah; Wang, Ye

    2012-01-01

    Action research has been recognized as a useful professional development tool for teaching, but for inservice teachers, conducting action research can be challenging. Their learning about action research can be influenced by social situations--whether in an MA (Master of Arts) program or other professional development. The purpose of this…

  6. The search and development of a new benchmarking tool for the grid

    CERN Document Server

    Stypka, Jan

    2014-01-01

    Paper describes a summer projecy which goal was to find a benchmarking tool that scales linearly to HepSpec06, but is free and widely available at the same time. In order to test potential candidates for this task, also an automatic system had to be rewritten and extended to run the benchmarks, manage data and visualise the results.

  7. Collaborating and delivering literature search results to clinical teams using web 2.0 tools.

    Science.gov (United States)

    Damani, Shamsha; Fulton, Stephanie

    2010-07-01

    This article describes the experiences of librarians at the Research Medical Library embedded within clinical teams at The University of Texas MD Anderson Cancer Center and their efforts to enhance communication within their teams using Web 2.0 tools. Pros and cons of EndNote Web, Delicious, Connotea, PBWorks, and SharePoint are discussed. PMID:20677061

  8. Monte Carlo-based searching as a tool to study carbohydrate structure.

    Science.gov (United States)

    Dowd, Michael K; Kiely, Donald E; Zhang, Jinsong

    2011-07-01

    A torsion angle-based Monte Carlo searching routine was developed and applied to several carbohydrate modeling problems. The routine was developed as a Unix shell script that calls several programs, which allows it to be interfaced with multiple potential functions and various utilities for evaluating conformers. In its current form, the program operates with several versions of the MM3 and MM4 molecular mechanics programs and has a module to calculate hydrogen-hydrogen coupling constants. The routine was used to study the low-energy exo-cyclic substituents of β-D-glucopyranose and the conformers of D-glucaramide, both of which had been previously studied with MM3 by full conformational searches. For these molecules, the program found all previously reported low-energy structures. The routine was also used to find favorable conformers of 2,3,4,5-tetra-O-acetyl-N,N'-dimethyl-D-glucaramide and D-glucitol, the latter of which is believed to have many low-energy forms. Finally, the technique was used to study the inter-ring conformations of β-gentiobiose, a β-(1→6)-linked disaccharide of D-glucopyranose. The program easily found conformers in the 10 previously identified low-energy regions for this disaccharide. In 6 of the 10 local regions, the same previously identified low-energy structures were found. In the remaining four regions, the search identified structures with slightly lower energies than those previously reported. The approach should be useful for extending modeling studies on acyclic monosaccharides and possibly oligosaccharides. PMID:21536262

  9. EC-BLAST: A Tool to Automatically Search and Compare Enzyme Reactions

    Science.gov (United States)

    Cuesta, Sergio Martinez; Furnham, Nicholas; Holliday, Gemma L.

    2014-01-01

    EC-BLAST is an algorithm for quantitative similarity searches between enzyme reactions at three levels a) bond change, b) reaction centre and c) reaction structure similarity. It exploits the knowledge of bond changes and reaction patterns for all known biochemical reactions derived from atom-atom mapping (AAM) across each reaction. This has the potential to improve the established enzyme classification system, to find novel biochemical transformations, to improve the assignment of enzyme function to sequences, as well as for the re-engineering of enzymes. EC-BLAST URL: http://www.ebi.ac.uk/thornton-srv/software/rbl/ PMID:24412978

  10. Neural Network Based Boolean Factor Analysis: Efficient Tool for Automated Topics Search.

    Czech Academy of Sciences Publication Activity Database

    Húsek, Dušan; Frolov, A. A.; Polyakov, P.Y.; Řezanková, H.

    Amman: Applied Science Private University, 2006 - (Issa, G.; El-Qawasmeh, E.; Raho, G.), s. 321-327 ISBN 9957-8592-0-X. [CSIT 2006. International Multiconference on Computer Science and Information Technology /4./. Amman (JO), 05.04.2006-07.04.2006] R&D Projects: GA AV ČR 1ET100300419 Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * neural networks * associative memory * clustering * web searching * semantic web * information retrieval * document indexing * document classification * document processing * data mining * machine learning Subject RIV: BB - Applied Statistics, Operational Research

  11. Forward search as a cryptanalytic tool against a public key privacy channel

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, G.J.; Holdridge, D.

    1982-01-01

    In symmetric cryptosystems that depend on a single (secret) key for both encryption and decryption, a cryptanalyst - since the key is unknown to him - must either work backward from the cipher or else from the cipher and some known pairs of plaintext messages and matching ciphers in attempting to recover the plaintext. In an asymmetric (two key) cryptosystem used in the public key, i.e., privacy channel, mode where the encryption key is publicly exposed so that anyone who wishes can encrypt messages that can only be decrypted by the person having the (secret) decryption key, a cryptanalytic weakness may occur that has no counterpart in symmetric systems. If the entropy of the input messages is too small (roughly speaking if it is computationally feasible to search through the most likely messages) either because the total number of messages is small or because a small number of the messages occur with high probabilities, the cryptanalyst can pre-encrypt these messages to form a cipher file that can then be matched against observed ciphers to accomplish a simple substitution decryption. This forward search cryptanalytic weakness of a public key privacy channel is purely a function of the entropy of the plaintext messages and does not depend on the existence of any cryptanalytic weakness in the concealment of the secret decryption key from a knowledge of the public encryption key in the underlying public key algorithm.

  12. Finding optimal interaction interface alignments between biological complexes

    KAUST Repository

    Cui, Xuefeng

    2015-06-13

    Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a \\'blackbox preprocessing\\' to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein-DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the \\'blackbox preprocessing\\'). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein-DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein-protein complex and a protein-RNA complex, which is biologically known as a protein-RNA mimicry case. © The Author 2015. Published by Oxford University Press.

  13. Image alignment

    Science.gov (United States)

    Dowell, Larry Jonathan

    2014-04-22

    Disclosed is a method and device for aligning at least two digital images. An embodiment may use frequency-domain transforms of small tiles created from each image to identify substantially similar, "distinguishing" features within each of the images, and then align the images together based on the location of the distinguishing features. To accomplish this, an embodiment may create equal sized tile sub-images for each image. A "key" for each tile may be created by performing a frequency-domain transform calculation on each tile. A information-distance difference between each possible pair of tiles on each image may be calculated to identify distinguishing features. From analysis of the information-distance differences of the pairs of tiles, a subset of tiles with high discrimination metrics in relation to other tiles may be located for each image. The subset of distinguishing tiles for each image may then be compared to locate tiles with substantially similar keys and/or information-distance metrics to other tiles of other images. Once similar tiles are located for each image, the images may be aligned in relation to the identified similar tiles.

  14. NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning.

    Science.gov (United States)

    Setoain, Javier; Franch, Mònica; Martínez, Marta; Tabas-Madrid, Daniel; Sorzano, Carlos O S; Bakker, Annette; Gonzalez-Couto, Eduardo; Elvira, Juan; Pascual-Montano, Alberto

    2015-07-01

    Drug repositioning, using known drugs for treating conditions different from those the drug was originally designed to treat, is an important drug discovery tool that allows for a faster and cheaper development process by using drugs that are already approved or in an advanced trial stage for another purpose. This is especially relevant for orphan diseases because they affect too few people to make drug research de novo economically viable. In this paper we present NFFinder, a bioinformatics tool for identifying potential useful drugs in the context of orphan diseases. NFFinder uses transcriptomic data to find relationships between drugs, diseases and a phenotype of interest, as well as identifying experts having published on that domain. The application shows in a dashboard a series of graphics and tables designed to help researchers formulate repositioning hypotheses and identify potential biological relationships between drugs and diseases. NFFinder is freely available at http://nffinder.cnb.csic.es. PMID:25940629

  15. PALM-IST: Pathway Assembly from Literature Mining - an Information Search Tool

    OpenAIRE

    Mandloi, Sapan; Chakrabarti, Saikat

    2015-01-01

    Manual curation of biomedical literature has become extremely tedious process due to its exponential growth in recent years. To extract meaningful information from such large and unstructured text, newer and more efficient mining tool is required. Here, we introduce PALM-IST, a computational platform that not only allows users to explore biomedical abstracts using keyword based text mining but also extracts biological entity (e.g., gene/protein, drug, disease, biological processes, cellular c...

  16. Grain Alignment and CMB Polarization Studies

    CERN Document Server

    Lazarian, A

    2008-01-01

    Polarized microwave emission from dust is an important foreground that may contaminate polarized CMB studies unless carefully accounted for. Modeling of polarization from dust requires a quantitative understanding of grain alignment. I review the current status of grain alignment theory outlining recent advances in quantitative description of the alignment. In particular, I show that the grain-alignment theory is a predictive one, and its results nicely match observations. Those indicate that the most important process of alignment is related to radiative torques acting on irregular grains. The recently developed analytical model of radiative torque alignment has proven to be a very efficient tool for predicting the degree of grain alignment. We expect the alignment theory to further mature before CMBPol flight, which would ensure a better accounting for the dust-related polarization. At the same time, CMBPol should provide the additional testing of grain alignment, clarifying the reliability of polarimetry f...

  17. MUSE optical alignment procedure

    Science.gov (United States)

    Laurent, Florence; Renault, Edgard; Loupias, Magali; Kosmalski, Johan; Anwand, Heiko; Bacon, Roland; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dubois, Jean-Pierre; Dupuy, Christophe; Kelz, Andreas; Lizon, Jean-Louis; Nicklas, Harald; Parès, Laurent; Remillieux, Alban; Seifert, Walter; Valentin, Hervé; Xu, Wenli

    2012-09-01

    MUSE (Multi Unit Spectroscopic Explorer) is a second generation VLT integral field spectrograph (1x1arcmin² Field of View) developed for the European Southern Observatory (ESO), operating in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently assembling and testing MUSE in the Integration Hall of the Observatoire de Lyon for the Preliminary Acceptance in Europe, scheduled for 2013. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic instrument mechanical structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2011, all MUSE subsystems were integrated, aligned and tested independently in each institute. After validations, the systems were shipped to the P.I. institute at Lyon and were assembled in the Integration Hall This paper describes the end-to-end optical alignment procedure of the MUSE instrument. The design strategy, mixing an optical alignment by manufacturing (plug and play approach) and few adjustments on key components, is presented. We depict the alignment method for identifying the optical axis using several references located in pupil and image planes. All tools required to perform the global alignment between each subsystem are described. The success of this alignment approach is demonstrated by the good results for the MUSE image quality. MUSE commissioning at the VLT (Very Large Telescope) is planned for 2013.

  18. Proteomics as the Tool to Search for Lung Disease Markers in Bronchoalveolar Lavage

    Directory of Open Access Journals (Sweden)

    Isabelle Noël-Georis

    2001-01-01

    Full Text Available Most lung disorders are known to be associated to considerable modifications of surfactant composition. Numerous of these abnormalities have been exploited in the past to diagnose lung diseases, allowing proper treatment and follow-up. Diagnosis was then based on phospholipid content, surface tension and cytological features of the epithelial lining fluid (ELF, sampled by bronchoalveolar lavage (BAL during fiberoscopic bronchoscopy. Today, it appears that the protein content of ELF displays a remarkably high complexity, not only due to the wide variety of the proteins it contains but also because of the great diversity of their cellular origins. The significance of the use of proteome analysis of BAL fluid for the search for new lung disease marker proteins and for their simultaneous display and analysis in patients suffering from lung disorders has been examined.

  19. Finding research information on the web: how to make the most of Google and other free search tools.

    Science.gov (United States)

    Blakeman, Karen

    2013-01-01

    The Internet and the World Wide Web has had a major impact on the accessibility of research information. The move towards open access and development of institutional repositories has resulted in increasing amounts of information being made available free of charge. Many of these resources are not included in conventional subscription databases and Google is not always the best way to ensure that one is picking up all relevant material on a topic. This article will look at how Google's search engine works, how to use Google more effectively for identifying research information, alternatives to Google and will review some of the specialist tools that have evolved to cope with the diverse forms of information that now exist in electronic form. PMID:23738438

  20. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    Kolář Michal

    2012-11-01

    Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

  1. THE METHOD OF APPLICATION OF A COLLECTIVE SEARCH ACTIVITY AS A TOOL DEVELOPING METHODOLOGICAL THINKING OF A TEACHER

    Directory of Open Access Journals (Sweden)

    Луиза Вахаевна Ибрагимова

    2013-04-01

    Full Text Available To realize any pedagogical theory into practice it is necessary to transform the theoretical concepts in teaching methods. The development of all abilities, including thinking, occurs only in the activity, which is specially organized by creating the required pedagogical conditions, in this case – it is a the application of enhanced mental activity in teachers training course and vocational training b establishment of a "virtual university" for teachers in an institute of professional training c the organization of interdisciplinary interaction of teachers, based on conditions of the nonlinear didactics (training teachers of different subjects. The presented method is implemented for two years and consists of three phases: the motivational and educational, intellectual and developmental, innovative and reflective. At the motivational and educational stage, possibilities of collective search activity actualize during the course of training, group goals are set and chosen methods of their achieving by using the first pedagogical conditions. At intellectual and developmental stage, the development of skills to the collective search for effective teaching decisions during intercourse training with the first-and second-pedagogical conditions is carried out. The innovative step is the promotion of teachers to self-determination of techniques and tools that improve the quality of the educational process, providing assistance to each other in the development of teaching manuals, which is achieved with the help of all three pedagogical conditions.DOI: http://dx.doi.org/10.12731/2218-7405-2013-2-17

  2. THE METHOD OF APPLICATION OF A COLLECTIVE SEARCH ACTIVITY AS A TOOL DEVELOPING METHODOLOGICAL THINKING OF A TEACHER

    Directory of Open Access Journals (Sweden)

    Ibragimova Luiza Vahaevna

    2013-02-01

    Full Text Available To realize any pedagogical theory into practice it is necessary to transform the theoretical concepts in teaching methods. The development of all abilities, including thinking, occurs only in the activity, which is specially organized by creating the required pedagogical conditions, in this case – it is a the application of enhanced mental activity in teachers training course and vocational training b establishment of a "virtual university" for teachers in an institute of professional training c the organization of interdisciplinary interaction of teachers, based on conditions of the nonlinear didactics (training teachers of different subjects. The presented method is implemented for two years and consists of three phases: the motivational and educational, intellectual and developmental, innovative and reflective. At the motivational and educational stage, possibilities of collective search activity actualize during the course of training, group goals are set and chosen methods of their achieving by using the first pedagogical conditions. At intellectual and developmental stage, the development of skills to the collective search for effective teaching decisions during intercourse training with the first-and second-pedagogical conditions is carried out. The innovative step is the promotion of teachers to self-determination of techniques and tools that improve the quality of the educational process, providing assistance to each other in the development of teaching manuals, which is achieved with the help of all three pedagogical conditions.

  3. Recode-2: new design, new search tools, and many more genes.

    LENUS (Irish Health Repository)

    Bekaert, Michaël

    2010-01-01

    \\'Recoding\\' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. Although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of \\'recoded\\' genes lags far behind annotation of \\'standard\\' genes. In order to address this issue, provide a service to researchers in the field, and offer training data for developers of gene-annotation software, we have gathered together known cases of recoding within the Recode database. Recode-2 is an improved and updated version of the database. It provides access to detailed information on genes known to utilize translational recoding and allows complex search queries, browsing of recoding data and enhanced visualization of annotated sequence elements. At present, the Recode-2 database stores information on approximately 1500 genes that are known to utilize recoding in their expression--a factor of approximately three increase over the previous version of the database. Recode-2 is available at http:\\/\\/recode.ucc.ie.

  4. A search for new hot subdwarf stars by means of Virtual Observatory tools II

    CERN Document Server

    Pérez-Fernández, Esther; Solano, Enrique; Oreiro, Raquel; Rodrigo, Carlos

    2016-01-01

    Recent massive sky surveys in different bandwidths are providing new opportunities to modern astronomy. The Virtual Observatory (VO) represents the adequate framework to handle the huge amount of information available and filter out data according to specific requirements. In this work, we applied a selection strategy to find new, uncatalogued hot subdwarfs making use of VO tools. We used large area catalogues (GALEX, SDSS, SuperCosmos, 2MASS) to retrieve photometric and astrometric information of stellar objects. To these objects, we applied colour and proper motion filters, together with an effective temperature cutoff, aimed at separating hot subdwarfs from other blue objects such as white dwarfs, cataclysmic variables or main sequence OB stars. As a result, we obtained 437 new, uncatalogued hot subdwarf candidates. Based on previous results, we expect our procedure to have an overall efficiency of at least 80 per cent. Visual inspection of the 68 candidates with SDSS spectrum showed that 65 can be classif...

  5. Adjusting scoring matrices to correct overextended alignments

    OpenAIRE

    Mills, Lauren J.; Pearson, William R.

    2013-01-01

    Motivation: Sequence similarity searches performed with BLAST, SSEARCH and FASTA achieve high sensitivity by using scoring matrices (e.g. BLOSUM62) that target low identity (33% identity). Adjusting the scoring matrix to reflect the identity of the homologous sequence can correct higher identity overextended alignment boundaries. In addition, the scoring matrix that produced a correct alignment could be reliably predicted based on the sequence identity seen in the original BLOSUM62 alignment....

  6. ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection

    Directory of Open Access Journals (Sweden)

    Alexandros Stamatakis

    2013-03-01

    Full Text Available Automated DNA sequencers generate chromatograms that contain raw sequencing data. They also generate data that translates the chromatograms into molecular sequences of A, C, G, T, or N (undetermined characters. Since chromatogram translation programs frequently introduce errors, a manual inspection of the generated sequence data is required. As sequence numbers and lengths increase, visual inspection and manual correction of chromatograms and corresponding sequences on a per-peak and per-nucleotide basis becomes an error-prone, time-consuming, and tedious process. Here, we introduce ChromatoGate (CG, an open-source software that accelerates and partially automates the inspection of chromatograms and the detection of sequencing errors for bidirectional sequencing runs. To provide users full control over the error correction process, a fully automated error correction algorithm has not been implemented. Initially, the program scans a given multiple sequence alignment (MSA for potential sequencing errors, assuming that each polymorphic site in the alignment may be attributed to a sequencing error with a certain probability. The guided MSA assembly procedure in ChromatoGate detects chromatogram peaks of all characters in an alignment that lead to polymorphic sites, given a user-defined threshold. The threshold value represents the sensitivity of the sequencing error detection mechanism. After this pre-filtering, the user only needs to inspect a small number of peaks in every chromatogram to correct sequencing errors. Finally, we show that correcting sequencing errors is important, because population genetic and phylogenetic inferences can be misled by MSAs with uncorrected mis-calls. Our experiments indicate that estimates of population mutation rates can be affected two- to three-fold by uncorrected errors.

  7. Searching for disease-modifying drugs in AD: can we combine neuropsychological tools with biological markers?

    Science.gov (United States)

    Caraci, Filippo; Castellano, Sabrina; Salomone, Salvatore; Drago, Filippo; Bosco, Paolo; Di Nuovo, Santo

    2014-02-01

    Drug discovery efforts in Alzheimer's disease (AD) have been directed in the last ten years to develop "disease-modifying drugs" able to exert neuroprotective effects in an early phase of AD pathogenesis. Unfortunately several candidate disease-modifying drugs have failed in Phase III clinical trials conducted in mild to moderate AD for different methodological difficulties, such as the time course of treatment in relation to development of disease as well as the appropriate use of validated biological and neuropsychological markers. Mild cognitive impairment (MCI) has been considered a precursor of AD. Much effort is now directed to identify the most appropriate and sensitive markers which can predict the progression from MCI to AD, such as neuroimaging markers (e.g. hippocampal atrophy and amyloid positron emission tomography imaging), cerebrospinal fluid markers (i.e. association of elevated tau with low levels of amyloid β -peptide(1-42) and neuropsychological markers (i.e. episodic memory deficits and executive dysfunction). Recent studies demonstrate that the combination of these different biomarkers significantly increases the chance to predict the conversion into AD within 24 months. These biomarkers will be essential in the future to analyze clinical efficacy of disease-modifying drugs in MCI patients at high risk to develop AD. In the present review we analyze recent evidence on the combination of neuropsychological and biological markers in AD as a new tool to track disease progression in early AD as well as the response to disease-modifying drugs. PMID:24040795

  8. IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data.

    Science.gov (United States)

    Sharman, Joanna L; Mpamhanga, Chidochangu P; Spedding, Michael; Germain, Pierre; Staels, Bart; Dacquet, Catherine; Laudet, Vincent; Harmar, Anthony J

    2011-01-01

    The IUPHAR database is an established online reference resource for several important classes of human drug targets and related proteins. As well as providing recommended nomenclature, the database integrates information on the chemical, genetic, functional and pathophysiological properties of receptors and ion channels, curated and peer-reviewed from the biomedical literature by a network of experts. The database now includes information on 616 gene products from four superfamilies in human and rodent model organisms: G protein-coupled receptors, voltage- and ligand-gated ion channels and, in a recent update, 49 nuclear hormone receptors (NHRs). New data types for NHRs include details on co-regulators, DNA binding motifs, target genes and 3D structures. Other recent developments include curation of the chemical structures of approximately 2000 ligand molecules, providing electronic descriptors, identifiers, link-outs and calculated molecular properties, all available via enhanced ligand pages. The interface now provides intelligent tools for the visualization and exploration of ligand structure-activity relationships and the structural diversity of compounds active at each target. The database is freely available at http://www.iuphar-db.org. PMID:21087994

  9. A search for new hot subdwarf stars by means of virtual observatory tools II

    Science.gov (United States)

    Pérez-Fernández, E.; Ulla, A.; Solano, E.; Oreiro, R.; Rodrigo, C.

    2016-04-01

    Recent massive sky surveys in different bandwidths are providing new opportunities to modern astronomy. The Virtual Observatory (VO) represents the adequate framework to handle the huge amount of information available and filter out data according to specific requirements. In this work, we applied a selection strategy to find new, uncatalogued hot subdwarfs making use of VO tools. We used large area catalogues like GALEX, Sloan Digital Sky Survey (SDSS), SuperCosmos and Two Micron All Sky Survey (2MASS) to retrieve photometric and astrometric information of stellar objects. To these objects, we applied colour and proper motion filters, together with an effective temperature cutoff, aimed at separating hot subdwarfs from other blue objects such as white dwarfs, cataclysmic variables or main-sequence OB stars. As a result, we obtained 437 new, uncatalogued hot subdwarf candidates. Based on previous results, we expect our procedure to have an overall efficiency of at least 80 per cent. Visual inspection of the 68 candidates with SDSS spectrum showed that 65 can be classified as hot subdwarfs: 5 sdOs, 25 sdOBs and 35 sdBs. This success rate above 95 per cent proves the robustness and efficiency of our methodology. The spectral energy distribution of 45 per cent of the subdwarf candidates showed infrared excesses, a signature of their probable binary nature. The stellar companions of the binary systems so detected are expected to be late-type main-sequence stars. A detailed determination of temperatures and spectral classification of the cool companions will be presented in a forthcoming work.

  10. Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments

    Energy Technology Data Exchange (ETDEWEB)

    Daily, Jeffrey A.

    2016-02-10

    Background: Sequence alignment algorithms are a key component of many bioinformatics applications. Though various fast Smith-Waterman local sequence alignment implementations have been developed for x86 CPUs, most are embedded into larger database search tools. In addition, fast implementations of Needleman-Wunsch global sequence alignment and its semi-global variants are not as widespread. This article presents the first software library for local, global, and semi-global pairwise intra-sequence alignments and improves the performance of previous intra-sequence implementations. Results: A faster intra-sequence pairwise alignment implementation is described and benchmarked. Using a 375 residue query sequence a speed of 136 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon E5-2670 12-core processor system, the highest reported for an implementation based on Farrar’s ’striped’ approach. When using only a single thread, parasail was 1.7 times faster than Rognes’s SWIPE. For many score matrices, parasail is faster than BLAST. The software library is designed for 64 bit Linux, OS X, or Windows on processors with SSE2, SSE41, or AVX2. Source code is available from https://github.com/jeffdaily/parasail under the Battelle BSD-style license. Conclusions: Applications that require optimal alignment scores could benefit from the improved performance. For the first time, SIMD global, semi-global, and local alignments are available in a stand-alone C library. Keywords: Smith-Waterman; Needleman-Wunsch; semi-global alignment; sequence alignment; SIMD; database search

  11. Chromatographic alignment by warping and dynamic programming as a pre-processing tool for PARAFAC modelling of liquid chromatography-mass spectrometry data.

    Science.gov (United States)

    Bylund, Dan; Danielsson, Rolf; Malmquist, Gunnar; Markides, Karin E

    2002-07-01

    Solutes analysed with LC-MS are characterised by their retention times and mass spectra, and quantified by the intensities measured. This highly selective information can be extracted by multiway modelling. However, for full use and interpretability it is necessary that the assumptions made for the model are valid. For PARAFAC modelling, the assumption is a trilinear data structure. With LC-MS, several factors, e.g. non-linear detector response and ionisation suppression may introduce deviations from trilinearity. The single largest problem, however, is the retention time shifts not related to the true sample variations. In this paper, a time warping algorithm for alignment of LC-MS data in the chromatographic direction has been examined. Several refinements have been implemented and the features are demonstrated for both simulated and real data. With moderate time shifts present in the data, pre-processing with this algorithm yields approximately trilinear data for which reasonable models can be made. PMID:12184621

  12. Protein structural similarity search by Ramachandran codes

    Directory of Open Access Journals (Sweden)

    Chang Chih-Hung

    2007-08-01

    Full Text Available Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation. SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.

  13. Web Search Engines

    OpenAIRE

    Rajashekar, TB

    1998-01-01

    The World Wide Web is emerging as an all-in-one information source. Tools for searching Web-based information include search engines, subject directories and meta search tools. We take a look at key features of these tools and suggest practical hints for effective Web searching.

  14. Using Student Reflections to Explore Curriculum Alignment

    OpenAIRE

    Marina Harvey; Chris Baumann

    2012-01-01

    The concept of curriculum alignment is held as a guiding principle of good curriculum design in higher education. Curriculum alignment can be mapped using a variety of strategies and tools. This paper reports on a project that expands the horizons of curriculum review by applying a novel methodology, word clouds, to investigate the use of student reflections for exploring curriculum alignment.Students, from Australia and Denmark, engaged in written reflections about their learning in a Busine...

  15. Using the open Web as an information resource and scholarly Web search engines as retrieval tools for academic and research purposes

    Directory of Open Access Journals (Sweden)

    Filistea Naude

    2010-08-01

    Full Text Available This study provided insight into the significance of the open Web as an information resource and Web search engines as research tools amongst academics. The academic staff establishment of the University of South Africa (Unisa was invited to participate in a questionnaire survey and included 1188 staff members from five colleges. This study culminated in a PhD dissertation in 2008. One hundred and eighty seven respondents participated in the survey which gave a response rate of 15.7%. The results of this study show that academics have indeed accepted the open Web as a useful information resource and Web search engines as retrieval tools when seeking information for academic and research work. The majority of respondents used the open Web and Web search engines on a daily or weekly basis to source academic and research information. The main obstacles presented by using the open Web and Web search engines included lack of time to search and browse the Web, information overload, poor network speed and the slow downloading speed of webpages.

  16. A comparison of four pair-wise sequence alignment methods

    OpenAIRE

    Essoussi, Nadia; Fayech, Sondes

    2007-01-01

    Protein sequence alignment has become an essential task in modern molecular biology research. A number of alignment techniques have been documented in literature and their corresponding tools are made available as freeware and commercial software. The choice and use of these tools for sequence alignment through the complete interpretation of alignment results is often considered non-trivial by end-users with limited skill in Bioinformatics algorithm development. Here, we discuss the compariso...

  17. Dissecting multiple sequence alignment methods : the analysis, design and development of generic multiple sequence alignment components in SeqAn

    OpenAIRE

    Rausch, T.

    2010-01-01

    Multiple sequence alignments are an indispensable tool in bioinformatics. Many applications rely on accurate multiple alignments, including protein structure prediction, phylogeny and the modeling of binding sites. In this thesis we dissected and analyzed the crucial algorithms and data structures required to construct such a multiple alignment. Based upon that dissection, we present a novel graph-based multiple sequence alignment program and a new method for multi-read alignments occurring i...

  18. Sambamba: fast processing of NGS alignment formats

    NARCIS (Netherlands)

    Tarasov, A.; Vilella, A.J.; Cuppen, E.; Nijman, I.J.; Prins, J.C.P.

    2015-01-01

    Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces proc

  19. Sambamba : Fast processing of NGS alignment formats

    NARCIS (Netherlands)

    Tarasov, Artem; Vilella, Albert J.; Cuppen, Edwin; Nijman, Isaac J.; Prins, Pjotr

    2015-01-01

    Summary: Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically red

  20. Methods and Tools to Align Curriculum to the Skills and Competencies Needed by the Workforce - an Example from Geospatial Science and Technology

    Science.gov (United States)

    Johnson, A. B.

    2012-12-01

    Geospatial science and technology (GST) including geographic information systems, remote sensing, global positioning systems and mobile applications, are valuable tools for geoscientists and students learning to become geoscientists. GST allows the user to analyze data spatially and temporarily and then visualize the data and outcomes in multiple formats (digital, web and paper). GST has evolved rapidly and it has been difficult to create effective curriculum as few guidelines existed to help educators. In 2010, the US Department of Labor (DoL), in collaboration with the National Geospatial Center of Excellence (GeoTech Center), a National Science Foundation supported grant, approved the Geospatial Technology Competency Mode (GTCM). The GTCM was developed and vetted with industry experts and provided the structure and example competencies needed across the industry. While the GTCM was helpful, a more detailed list of skills and competencies needed to be identified in order to build appropriate curriculum. The GeoTech Center carried out multiple DACUM events to identify the skills and competencies needed by entry-level workers. DACUM (Developing a Curriculum) is a job analysis process whereby expert workers are convened to describe what they do for a specific occupation. The outcomes from multiple DACUMs were combined into a MetaDACUM and reviewed by hundreds of GST professionals. This provided a list of more than 320 skills and competencies needed by the workforce. The GeoTech Center then held multiple workshops across the U.S. where more than 100 educators knowledgeable in teaching GST parsed the list into Model Courses and a Model Certificate Program. During this process, tools were developed that helped educators define which competency should be included in a specific course and the depth of instruction for that competency. This presentation will provide details about the process, methodology and tools used to create the Models and suggest how they can be used

  1. Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

    Energy Technology Data Exchange (ETDEWEB)

    Mohammadi, Shahin [Purdue Univ., West Lafayette, IN (United States); Gleich, David F. [Purdue Univ., West Lafayette, IN (United States); Kolda, Tamara G. [Sandia National Laboratories (SNL-CA), Livermore, CA (United States); Grama, Ananth [Purdue Univ., West Lafayette, IN (United States)

    2015-11-01

    Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangular AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.

  2. Using the open Web as an information resource and scholarly Web search engines as retrieval tools for academic and research purposes

    OpenAIRE

    Filistea Naude; Chris Rensleigh; Adeline S.A. du Toit

    2010-01-01

    This study provided insight into the significance of the open Web as an information resource and Web search engines as research tools amongst academics. The academic staff establishment of the University of South Africa (Unisa) was invited to participate in a questionnaire survey and included 1188 staff members from five colleges. This study culminated in a PhD dissertation in 2008. One hundred and eighty seven respondents participated in the survey which gave a response rate of 15.7%. The re...

  3. Functionality Pattern Matching as an Efficient Complementary Structure/Reaction Search Tool: an Open-Source Approach

    Directory of Open Access Journals (Sweden)

    Norbert Haider

    2010-07-01

    Full Text Available An open-source software package for creating and operating web-based structure and/or reaction databases is presented. Besides standard search capabilities (text, structure/substructure/similarity, the system offers a fast additional search option, entirely based on binary pattern matching, which uses automatically assigned functional group descriptors.

  4. Searching algorithm for type IV secretion system effectors 1.0: a tool for predicting type IV effectors and exploring their genomic context.

    Science.gov (United States)

    Meyer, Damien F; Noroy, Christophe; Moumène, Amal; Raffaele, Sylvain; Albina, Emmanuel; Vachiéry, Nathalie

    2013-11-01

    Type IV effectors (T4Es) are proteins produced by pathogenic bacteria to manipulate host cell gene expression and processes, divert the cell machinery for their own profit and circumvent the immune responses. T4Es have been characterized for some bacteria but many remain to be discovered. To help biologists identify putative T4Es from the complete genome of α- and γ-proteobacteria, we developed a Perl-based command line bioinformatics tool called S4TE (searching algorithm for type-IV secretion system effectors). The tool predicts and ranks T4E candidates by using a combination of 13 sequence characteristics, including homology to known effectors, homology to eukaryotic domains, presence of subcellular localization signals or secretion signals, etc. S4TE software is modular, and specific motif searches are run independently before ultimate combination of the outputs to generate a score and sort the strongest T4Es candidates. The user keeps the possibility to adjust various searching parameters such as the weight of each module, the selection threshold or the input databases. The algorithm also provides a GC% and local gene density analysis, which strengthen the selection of T4E candidates. S4TE is a unique predicting tool for T4Es, finding its utility upstream from experimental biology. PMID:23945940

  5. A new bioinformatics analysis tools framework at EMBL–EBI

    OpenAIRE

    Goujon, Mickael; McWilliam, Hamish; Li, Weizhong; Valentin, Franck; Squizzato, Silvano; Paern, Juri; Lopez, Rodrigo

    2010-01-01

    The EMBL-EBI provides access to various mainstream sequence analysis applications. These include sequence similarity search services such as BLAST, FASTA, InterProScan and multiple sequence alignment tools such as ClustalW, T-Coffee and MUSCLE. Through the sequence similarity search services, the users can search mainstream sequence databases such as EMBL-Bank and UniProt, and more than 2000 completed genomes and proteomes. We present here a new framework aimed at both novice as well as exper...

  6. Improving protein structure similarity searches using domain boundaries based on conserved sequence information

    OpenAIRE

    Madej Tom; Wang Yanli; Thompson Kenneth; Bryant Stephen H

    2009-01-01

    Abstract Background The identification of protein domains plays an important role in protein structure comparison. Domain query size and composition are critical to structure similarity search algorithms such as the Vector Alignment Search Tool (VAST), the method employed for computing related protein structures in NCBI Entrez system. Currently, domains identified on the basis of structural compactness are used for VAST computations. In this study, we have investigated how alternative definit...

  7. In search of the AHA! - Creating a service experience visualisation tool for service design first-timers

    OpenAIRE

    Isosaari, Jukka

    2015-01-01

    The service design as an industry has developed a set of service process visualisation tools already from the 1980’s. The tools have had a strong aim on mapping all the factors that affect on the service process. The companies working among service design have often also created own versions of the tools. These issues together have created a situation in which the service designers provide complicated service visualisations in various styles and their new clients have problems understanding ...

  8. A Real-Time All-Atom Structural Search Engine for Proteins

    OpenAIRE

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

    2014-01-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designabilit...

  9. On comparing two structured RNA multiple alignments.

    Science.gov (United States)

    Patel, Vandanaben; Wang, Jason T L; Setia, Shefali; Verma, Anurag; Warden, Charles D; Zhang, Kaizhong

    2010-12-01

    We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at http://bioinformatics.njit.edu/blockmatch. A jar file of the program is also available for download from the web server. PMID:21121021

  10. Students are Confident Using Federated Search Tools as much as Single Databases. A Review of: Armstrong, A. (2009. Student perceptions of federated searching vs. single database searching. Reference Services Review, 37(3, 291-303. doi:10.1108/00907320910982785

    Directory of Open Access Journals (Sweden)

    Deena Yanofsky

    2011-09-01

    Full Text Available Objective – To measure students’ perceptions of the ease-of-use and efficacy of a federated search tool versus a single multidisciplinary database.Design – An evaluation worksheet, employing a combination of quantitative and qualitative questions.Setting – A required, first-year English composition course taught at the University of Illinois at Chicago (UIC.Subjects – Thirty-one undergraduate students completed and submitted the worksheet.Methods – Students attended two library instruction sessions. The first session introduced participants to basic Boolean searching (using AND only, selecting appropriate keywords and searching for books in the library catalogue. In the second library session, students were handed an evaluation worksheet and, with no introduction to the process of searching article databases, were asked to find relevant articles on a research topic of their own choosing using both a federated search tool and a single multidisciplinary database. The evaluation worksheet was divided into four sections: step-by-step instructions for accessing the single multidisciplinary database and the federated search tool; space to record search strings in both resources; space to record the titles of up to five relevant articles; and a series of quantitative and qualitative questions regarding ease-of-use, relevancy of results, overall preference (if any between the two resources, likeliness of future use and other preferred research tools. Half of the participants received a worksheet with instructions to search the federated search tool before the single database; the order was reversed for the other half of the students. The evaluation worksheet was designed to be completed in one hour.Participant responses to qualitative questions were analyzed, codified and grouped into thematic categories. If a student mentioned more than one factor in responding to a question, their response was recorded in multiple categories.Main Results

  11. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and J. Pivarski

    2011-01-01

    Alignment efforts in the first few months of 2011 have shifted away from providing alignment constants (now a well established procedure) and focussed on some critical remaining issues. The single most important task left was to understand the systematic differences observed between the track-based (TB) and hardware-based (HW) barrel alignments: a systematic difference in r-φ and in z, which grew as a function of z, and which amounted to ~4-5 mm differences going from one end of the barrel to the other. This difference is now understood to be caused by the tracker alignment. The systematic differences disappear when the track-based barrel alignment is performed using the new “twist-free” tracker alignment. This removes the largest remaining source of systematic uncertainty. Since the barrel alignment is based on hardware, it does not suffer from the tracker twist. However, untwisting the tracker causes endcap disks (which are aligned ...

  12. Multiple sequence alignment accuracy and evolutionary distance estimation

    OpenAIRE

    Rosenberg Michael S

    2005-01-01

    Abstract Background Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and never with the control provided by simulation analysis. This study used sequence simulation to examine the gain in accuracy of adding a third sequence to a pair wise alignment, particularly concentrating on how the phylogenetic positio...

  13. Open-Source Tools for Enhancing Full-Text Searching of OPACs: Use of Koha, Greenstone and Fedora

    Science.gov (United States)

    Anuradha, K. T.; Sivakaminathan, R.; Kumar, P. Arun

    2011-01-01

    Purpose: There are many library automation packages available as open-source software, comprising two modules: staff-client module and online public access catalogue (OPAC). Although the OPAC of these library automation packages provides advanced features of searching and retrieval of bibliographic records, none of them facilitate full-text…

  14. Using Student Reflections to Explore Curriculum Alignment

    Directory of Open Access Journals (Sweden)

    Marina Harvey

    2012-10-01

    Full Text Available The concept of curriculum alignment is held as a guiding principle of good curriculum design in higher education. Curriculum alignment can be mapped using a variety of strategies and tools. This paper reports on a project that expands the horizons of curriculum review by applying a novel methodology, word clouds, to investigate the use of student reflections for exploring curriculum alignment.Students, from Australia and Denmark, engaged in written reflections about their learning in a Business Brand Marketing subject. These reflections provide the data that is analysed for its alignment with the subject’s learning outcomes. The word cloud analysis is found to be useful in providing evidence of curriculum alignment and indicators for directing deeper textual analysis.

  15. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2010-01-01

    The main developments in muon alignment since March 2010 have been the production, approval and deployment of alignment constants for the ICHEP data reprocessing. In the barrel, a new geometry, combining information from both hardware and track-based alignment systems, has been developed for the first time. The hardware alignment provides an initial DT geometry, which is then anchored as a rigid solid, using the link alignment system, to a reference frame common to the tracker. The “GlobalPositionRecords” for both the Tracker and Muon systems are being used for the first time, and the initial tracker-muon relative positioning, based on the link alignment, yields good results within the photogrammetry uncertainties of the Tracker and alignment ring positions. For the first time, the optical and track-based alignments show good agreement between them; the optical alignment being refined by the track-based alignment. The resulting geometry is the most complete to date, aligning all 250 DTs, ...

  16. Architectural Refactoring for Fast and Modular Bioinformatics Sequence Search

    OpenAIRE

    Archuleta, Jeremy; Tilevich, Eli; Feng, Wu-chun

    2006-01-01

    Bioinformaticists use the Basic Local Alignment Search Tool (BLAST) to characterize an unknown sequence by comparing it against a database of known sequences, thus detecting evolutionary relationships and biological properties. mpiBLAST is a widely-used, high-performance, open-source parallelization of BLAST that runs on a computer cluster delivering super-linear speedups. However, the Achilles heel of mpiBLAST is its lack of modularity, adversely affecting maintainability and extensibili...

  17. Aligning sourcing activities with corporate strategy

    OpenAIRE

    Buczek, Kristopher

    2014-01-01

    In this paper I set out to discover how global firms ensure that sourcing activities are aligned with corporate strategy. In order to understand this, I broke the problem down into three specific questions, which were: 1) How does strategy flow through the sourcing departments of large firms? 2) What hurdles do sourcing departments face when trying to implement corporate strategy? 3) What tools are available in improving the alignment between corporate strategies and sourcing activi...

  18. FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines.

    Science.gov (United States)

    Wedge, David C; Krishna, Ritesh; Blackhurst, Paul; Siepen, Jennifer A; Jones, Andrew R; Hubbard, Simon J

    2011-04-01

    Confident identification of peptides via tandem mass spectrometry underpins modern high-throughput proteomics. This has motivated considerable recent interest in the postprocessing of search engine results to increase confidence and calculate robust statistical measures, for example through the use of decoy databases to calculate false discovery rates (FDR). FDR-based analyses allow for multiple testing and can assign a single confidence value for both sets and individual peptide spectrum matches (PSMs). We recently developed an algorithm for combining the results from multiple search engines, integrating FDRs for sets of PSMs made by different search engine combinations. Here we describe a web-server and a downloadable application that makes this routinely available to the proteomics community. The web server offers a range of outputs including informative graphics to assess the confidence of the PSMs and any potential biases. The underlying pipeline also provides a basic protein inference step, integrating PSMs into protein ambiguity groups where peptides can be matched to more than one protein. Importantly, we have also implemented full support for the mzIdentML data standard, recently released by the Proteomics Standards Initiative, providing users with the ability to convert native formats to mzIdentML files, which are available to download. PMID:21222473

  19. Structural analysis of aligned RNAs.

    Science.gov (United States)

    Voss, Björn

    2006-01-01

    The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de. PMID:17020924

  20. Le modèle probabiliste de l'alignement local de deux séquences

    OpenAIRE

    Nicodème, Pierre

    1997-01-01

    Nous décrivons le modèle probabiliste utilisé pour calibrer l'alignement local de deux séquences, quand un schéma de score additif est utilisé. Ce modèle est utilisé en particulier par le logiciel BLAST (Basic Local Alignment Search Tool), qui est employé fréquemment par les biologistes. Asymptotiquement, la probabilité associée au score d'un alignement optimal vérifie une loi des valeurs extrêmes. Nous analysons différents aspects des outils mathématiques (modèles de marche aléatoire, décomp...

  1. Developing a Data Discovery Tool for Interdisciplinary Science: Leveraging a Web-based Mapping Application and Geosemantic Searching

    Science.gov (United States)

    Albeke, S. E.; Perkins, D. G.; Ewers, S. L.; Ewers, B. E.; Holbrook, W. S.; Miller, S. N.

    2015-12-01

    The sharing of data and results is paramount for advancing scientific research. The Wyoming Center for Environmental Hydrology and Geophysics (WyCEHG) is a multidisciplinary group that is driving scientific breakthroughs to help manage water resources in the Western United States. WyCEHG is mandated by the National Science Foundation (NSF) to share their data. However, the infrastructure from which to share such diverse, complex and massive amounts of data did not exist within the University of Wyoming. We developed an innovative framework to meet the data organization, sharing, and discovery requirements of WyCEHG by integrating both open and closed source software, embedded metadata tags, semantic web technologies, and a web-mapping application. The infrastructure uses a Relational Database Management System as the foundation, providing a versatile platform to store, organize, and query myriad datasets, taking advantage of both structured and unstructured formats. Detailed metadata are fundamental to the utility of datasets. We tag data with Uniform Resource Identifiers (URI's) to specify concepts with formal descriptions (i.e. semantic ontologies), thus allowing users the ability to search metadata based on the intended context rather than conventional keyword searches. Additionally, WyCEHG data are geographically referenced. Using the ArcGIS API for Javascript, we developed a web mapping application leveraging database-linked spatial data services, providing a means to visualize and spatially query available data in an intuitive map environment. Using server-side scripting (PHP), the mapping application, in conjunction with semantic search modules, dynamically communicates with the database and file system, providing access to available datasets. Our approach provides a flexible, comprehensive infrastructure from which to store and serve WyCEHG's highly diverse research-based data. This framework has not only allowed WyCEHG to meet its data stewardship

  2. Implementation of a Parallel Protein Structure Alignment Service on Cloud

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2013-01-01

    Full Text Available Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

  3. Implementation of a parallel protein structure alignment service on cloud.

    Science.gov (United States)

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

  4. Search Engines for Tomorrow's Scholars

    Science.gov (United States)

    Fagan, Jody Condit

    2011-01-01

    Today's scholars face an outstanding array of choices when choosing search tools: Google Scholar, discipline-specific abstracts and index databases, library discovery tools, and more recently, Microsoft's re-launch of their academic search tool, now dubbed Microsoft Academic Search. What are these tools' strengths for the emerging needs of…

  5. Fast Statistical Alignment

    OpenAIRE

    Bradley, Robert K.; Adam Roberts; Michael Smoot; Sudeep Juvekar; Jaeyoung Do; Colin Dewey; Ian Holmes; Lior Pachter

    2009-01-01

    We describe a new program for the alignment of multiple biological sequences that is both statistically motivated and fast enough for problem sizes that arise in practice. Our Fast Statistical Alignment program is based on pair hidden Markov models which approximate an insertion/deletion process on a tree and uses a sequence annealing algorithm to combine the posterior probabilities estimated from these models into a multiple alignment. FSA uses its explicit statistical model to produce multi...

  6. Horizontal carbon nanotube alignment.

    Science.gov (United States)

    Cole, Matthew T; Cientanni, Vito; Milne, William I

    2016-09-21

    The production of horizontally aligned carbon nanotubes offers a rapid means of realizing a myriad of self-assembled near-atom-scale technologies - from novel photonic crystals to nanoscale transistors. The ability to reproducibly align anisotropic nanostructures has huge technological value. Here we review the present state-of-the-art in horizontal carbon nanotube alignment. For both in and ex situ approaches, we quantitatively assess the reported linear packing densities alongside the degree of alignment possible for each of these core methodologies. PMID:27546174

  7. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2010-01-01

    Most of the work in muon alignment since December 2009 has focused on the geometry reconstruction from the optical systems and improvements in the internal alignment of the DT chambers. The barrel optical alignment system has progressively evolved from reconstruction of single active planes to super-planes (December 09) to a new, full barrel reconstruction. Initial validation studies comparing this full barrel alignment at 0T with photogrammetry provide promising results. In addition, the method has been applied to CRAFT09 data, and the resulting alignment at 3.8T yields residuals from tracks (extrapolated from the tracker) which look smooth, suggesting a good internal barrel alignment with a small overall offset with respect to the tracker. This is a significant improvement, which should allow the optical system to provide a start-up alignment for 2010. The end-cap optical alignment has made considerable progress in the analysis of transfer line data. The next set of alignment constants for CSCs will there...

  8. Orthodontics and Aligners

    Science.gov (United States)

    ... Repairing Chipped Teeth Teeth Whitening Tooth-Colored Fillings Orthodontics and Aligners Straighten teeth for a healthier smile. Orthodontics When consumers think about orthodontics, braces are the ...

  9. Optical alignments of the Cosmic Background Explorer (COBE) observatory

    Science.gov (United States)

    Sampler, Henry P.

    1990-01-01

    The angular alignments and stabilities of multiple components in a single coordinate system were determined using various alignment tooling techniques. These techniques use autocollimation measurements with a first order theodolite and transformation of coordinates to determine the relative alignment between various components with respect to a common set of COBE spacecraft coordinate axes. Optical-mechanical alignment techniques were also used to integrate the flight COBE observatory attitude control system module that consists of gyros, reaction wheels, and a momentum wheel. Particular attention is given to the techniques for alignments and stabilities of the earth scanners, sun sensors, far IR absolute spectrophotometer, Diffuse Infrared Background Experiment, and differential microwave radiometer antenna horn boresights.

  10. Monolingual alignment with moves for genetic criticism Alignement monolingue avec recherche de déplacements pour la critique génétique

    Directory of Open Access Journals (Sweden)

    Julien Bourdaillet

    2010-01-01

    Full Text Available This paper describes the problem of monolingual alignment with search for displaced segments (hereafter called move search. It occurs in genetic criticism, a subfield of literary studies. Existing alignment applications fare poorly on this NP-hard problem. We propose to borrow a family of algorithms from bioinformatics and text algorithmics called fragment chaining alignment. An adaptation of this type of algorithms to NLP is described. Our method enables us to align a pair of texts with move search at the character level. It works for any alphabetic language and achieves scalability. An experimental evaluation presents the good results we obtained compared to other approaches.

  11. Considerations in the identification of functional RNA structural elements in genomic alignments

    Directory of Open Access Journals (Sweden)

    Blencowe Benjamin J

    2007-01-01

    Full Text Available Abstract Background Accurate identification of novel, functional noncoding (nc RNA features in genome sequence has proven more difficult than for exons. Current algorithms identify and score potential RNA secondary structures on the basis of thermodynamic stability, conservation, and/or covariance in sequence alignments. Neither the algorithms nor the information gained from the individual inputs have been independently assessed. Furthermore, due to issues in modelling background signal, it has been difficult to gauge the precision of these algorithms on a genomic scale, in which even a seemingly small false-positive rate can result in a vast excess of false discoveries. Results We developed a shuffling algorithm, shuffle-pair.pl, that simultaneously preserves dinucleotide frequency, gaps, and local conservation in pairwise sequence alignments. We used shuffle-pair.pl to assess precision and recall of six ncRNA search tools (MSARI, QRNA, ddbRNA, RNAz, Evofold, and several variants of simple thermodynamic stability on a test set of 3046 alignments of known ncRNAs. Relative to mononucleotide shuffling, preservation of dinucleotide content in shuffling the alignments resulted in a drastic increase in estimated false-positive detection rates for ncRNA elements, precluding evaluation of higher order alignments, which cannot not be adequately shuffled maintaining both dinucleotides and alignment structure. On pairwise alignments, none of the covariance-based tools performed markedly better than thermodynamic scoring alone. Although the high false-positive rates call into question the veracity of any individual predicted secondary structural element in our analysis, we nevertheless identified intriguing global trends in human genome alignments. The distribution of ncRNA prediction scores in 75-base windows overlapping UTRs, introns, and intergenic regions analyzed using both thermodynamic stability and EvoFold (which has no thermodynamic component was

  12. Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements

    Directory of Open Access Journals (Sweden)

    Neumann Steffen

    2008-09-01

    Full Text Available Abstract Background Liquid chromatography coupled to mass spectrometry (LC-MS has become a prominent tool for the analysis of complex proteomics and metabolomics samples. In many applications multiple LC-MS measurements need to be compared, e. g. to improve reliability or to combine results from different samples in a statistical comparative analysis. As in all physical experiments, LC-MS data are affected by uncertainties, and variability of retention time is encountered in all data sets. It is therefore necessary to estimate and correct the underlying distortions of the retention time axis to search for corresponding compounds in different samples. To this end, a variety of so-called LC-MS map alignment algorithms have been developed during the last four years. Most of these approaches are well documented, but they are usually evaluated on very specific samples only. So far, no publication has been assessing different alignment algorithms using a standard LC-MS sample along with commonly used quality criteria. Results We propose two LC-MS proteomics as well as two LC-MS metabolomics data sets that represent typical alignment scenarios. Furthermore, we introduce a new quality measure for the evaluation of LC-MS alignment algorithms. Using the four data sets to compare six freely available alignment algorithms proposed for the alignment of metabolomics and proteomics LC-MS measurements, we found significant differences with respect to alignment quality, running time, and usability in general. Conclusion The multitude of available alignment methods necessitates the generation of standard data sets and quality measures that allow users as well as developers to benchmark and compare their map alignment tools on a fair basis. Our study represents a first step in this direction. Currently, the installation and evaluation of the "correct" parameter settings can be quite a time-consuming task, and the success of a particular method is still highly

  13. BLAST: at the core of a powerful and diverse set of sequence analysis tools.

    Science.gov (United States)

    McGinnis, Scott; Madden, Thomas L

    2004-07-01

    Basic Local Alignment Search Tool (BLAST) is one of the most heavily used sequence analysis tools available in the public domain. There is now a wide choice of BLAST algorithms that can be used to search many different sequence databases via the BLAST web pages (http://www.ncbi.nlm.nih.gov/BLAST/). All the algorithm-database combinations can be executed with default parameters or with customized settings, and the results can be viewed in a variety of ways. A new online resource, the BLAST Program Selection Guide, has been created to assist in the definition of search strategies. This article discusses optimal search strategies and highlights some BLAST features that can make your searches more powerful. PMID:15215342

  14. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    The main progress of the muon alignment group since March has been in the refinement of both the track-based alignment for the DTs and the hardware-based alignment for the CSCs. For DT track-based alignment, there has been significant improvement in the internal alignment of the superlayers inside the DTs. In particular, the distance between superlayers is now corrected, eliminating the residual dependence on track impact angles, and good agreement is found between survey and track-based corrections. The new internal geometry has been approved to be included in the forthcoming reprocessing of CRAFT samples. The alignment of DTs with respect to the tracker using global tracks has also improved significantly, since the algorithms use the latest B-field mapping, better run selection criteria, optimized momentum cuts, and an alignment is now obtained for all six degrees of freedom (three spatial coordinates and three rotations) of the aligned DTs. This work is ongoing and at a stage where we are trying to unders...

  15. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    2011-01-01

    The Muon Alignment work now focuses on producing a new track-based alignment with higher track statistics, making systematic studies between the results of the hardware and track-based alignment methods and aligning the barrel using standalone muon tracks. Currently, the muon track reconstruction software uses a hardware-based alignment in the barrel (DT) and a track-based alignment in the endcaps (CSC). An important task is to assess the muon momentum resolution that can be achieved using the current muon alignment, especially for highly energetic muons. For this purpose, cosmic ray muons are used, since the rate of high-energy muons from collisions is very low and the event statistics are still limited. Cosmics have the advantage of higher statistics in the pT region above 100 GeV/c, but they have the disadvantage of having a mostly vertical topology, resulting in a very few global endcap muons. Only the barrel alignment has therefore been tested so far. Cosmic muons traversing CMS from top to bottom are s...

  16. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    Since December, the muon alignment community has focused on analyzing the data recorded so far in order to produce new DT and CSC Alignment Records for the second reprocessing of CRAFT data. Two independent algorithms were developed which align the DT chambers using global tracks, thus providing, for the first time, a relative alignment of the barrel with respect to the tracker. These results are an important ingredient for the second CRAFT reprocessing and allow, for example, a more detailed study of any possible mis-modelling of the magnetic field in the muon spectrometer. Both algorithms are constructed in such a way that the resulting alignment constants are not affected, to first order, by any such mis-modelling. The CSC chambers have not yet been included in this global track-based alignment due to a lack of statistics, since only a few cosmics go through the tracker and the CSCs. A strategy exists to align the CSCs using the barrel as a reference until collision tracks become available. Aligning the ...

  17. Real Interference Alignment

    CERN Document Server

    Motahari, Abolfazl Seyed; Maddah-Ali, Mohammad-Ali; Khandani, Amir Keyvan

    2010-01-01

    In this paper, we show that the total Degrees-Of-Freedoms (DOF) of the $K$-user Gaussian Interference Channel (GIC) can be achieved by incorporating a new alignment technique known as \\emph{real interference alignment}. This technique compared to its ancestor \\emph{vector interference alignment} performs on a single real line and exploits the properties of real numbers to provide optimal signaling. The real interference alignment relies on a new coding scheme in which several data streams having fractional multiplexing gains are sent by transmitters and interfering streams are aligned at receivers. The coding scheme is backed up by a recent result in the field of Diophantine approximation, which states that the convergence part of the Khintchine-Groshev theorem holds for points on non-degenerate manifolds.

  18. Students are Confident Using Federated Search Tools as much as Single Databases. A Review of: Armstrong, A. (2009). Student perceptions of federated searching vs. single database searching. Reference Services Review, 37(3), 291-303. doi:10.1108/00907320910982785

    OpenAIRE

    Deena Yanofsky

    2011-01-01

    Objective – To measure students’ perceptions of the ease-of-use and efficacy of a federated search tool versus a single multidisciplinary database.Design – An evaluation worksheet, employing a combination of quantitative and qualitative questions.Setting – A required, first-year English composition course taught at the University of Illinois at Chicago (UIC).Subjects – Thirty-one undergraduate students completed and submitted the worksheet.Methods – Students attended two library instruction s...

  19. Search for magnetic minerals in Martian rocks: Overview of the Rock Abrasion Tool (RAT) magnet investigation on Spirit and Opportunity

    Science.gov (United States)

    Goetz, Walter; Leer, Kristoffer; Gunnlaugsson, Haraldur P.; Bartlett, Paul; Basso, Brandon; Bell, Jim; Bertelsen, Preben; Binau, Charlotte S.; Chu, Phillip C.; Gorevan, S.; Hansen, Mikkel F.; Hviid, Stubbe F.; Kinch, Kjartan M.; Klingelhöfer, Göstar; Kusack, Alastair; Madsen, Morten B.; Ming, Douglas W.; Morris, Richard V.; Mumm, Erik; Myrick, Tom; Olsen, Malte; Squyres, Steven W.; Wilson, Jack; Yen, Albert

    2008-05-01

    The Rock Abrasion Tool (RAT) on board the Mars Exploration Rovers (MER) is a grinding tool designed to remove dust coatings and/or weathering rinds from rocks and expose fresh rock material. Four magnets of different strengths that are built into the structure of the RAT have been attracting substantial amounts of magnetic material during RAT activities from rocks throughout both rover missions. The RAT magnet experiment as performed on Spirit demonstrates the presence of a strongly ferrimagnetic phase in Gusev crater rocks, which based on Mössbauer and visible/near-infrared reflectance spectra is interpreted as magnetite. The amount of abraded rock material adhering to the magnets varied strongly during the mission and is correlated in a consistent way to the amount of magnetite inferred from Mössbauer spectra for the corresponding rock. The RAT magnet experiment as performed on Opportunity also indicates the presence of a strongly ferrimagnetic phase in outcrops, such as magnetite or an altered version of magnetite. However, the evidence is weaker than in the case of Spirit. According to data from the α particle X-ray spectrometer (APXS) and the Mössbauer spectrometer (MB), the Eagle crater outcrops should not contain magnetite and their magnetization should not exceed 0.03 A m2 kg-1. However, this assertion seems to be in contradiction with the results of the RAT magnet experiment. The evidence for a strongly ferrimagnetic phase at low abundance in the Meridiani outcrops is discussed.

  20. MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa

    Science.gov (United States)

    D'Onorio de Meo, Paolo; D'Antonio, Mattia; Griggio, Francesca; Lupi, Renato; Borsani, Massimiliano; Pavesi, Giulio; Castrignanò, Tiziana; Pesole, Graziano; Gissi, Carmela

    2012-01-01

    The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa. PMID:22123747

  1. Automatic generation of alignments for 3D QSAR analyses.

    Science.gov (United States)

    Jewell, N E; Turner, D B; Willett, P; Sexton, G J

    2001-01-01

    Many 3D QSAR methods require the alignment of the molecules in a dataset, which can require a fair amount of manual effort in deciding upon a rational basis for the superposition. This paper describes the use of FBSS, a program for field-based similarity searching in chemical databases, for generating such alignments automatically. The CoMFA and CoMSIA experiments with several literature datasets show that the QSAR models resulting from the FBSS alignments are broadly comparable in predictive performance with the models resulting from manual alignments. PMID:11774998

  2. Finite-size scaling as a tool in the search for the QCD critical point in heavy ion data

    International Nuclear Information System (INIS)

    Given the short lifetime and small volume of the quark-gluon plasma (QGP) formed in heavy ion collisions, a possible critical endpoint (CEP) will be blurred in a region and the effects from criticality severely smoothened. Nevertheless, the nonmonotonic behavior of correlation functions near criticality for systems of different sizes, given by different centralities in heavy ion collisions, must obey finite-size scaling. We apply the predicting power of scaling plots to the search for the CEP of strong interactions using data from heavy ion collisions at RHIC. The results of our data analysis exclude a critical point below chemical potentials μ∼400 MeV. Extrapolating the analysis, we speculate that criticality could appear slightly above μ∼500 MeV. Using available data we extrapolate our scaling curves to predict the behavior of new data at lower center-of-mass energy, currently being investigated in the Beam Energy Scan program at RHIC. If heavy-ion collisions drop out of the QGP phase before the CEP is reached, finite-size scaling might be the only way to experimentally estimate its position in the phase diagram.

  3. BBMap: A Fast, Accurate, Splice-Aware Aligner

    Energy Technology Data Exchange (ETDEWEB)

    Bushnell, Brian

    2014-03-17

    Alignment of reads is one of the primary computational tasks in bioinformatics. Of paramount importance to resequencing, alignment is also crucial to other areas - quality control, scaffolding, string-graph assembly, homology detection, assembly evaluation, error-correction, expression quantification, and even as a tool to evaluate other tools. An optimal aligner would greatly improve virtually any sequencing process, but optimal alignment is prohibitively expensive for gigabases of data. Here, we will present BBMap [1], a fast splice-aware aligner for short and long reads. We will demonstrate that BBMap has superior speed, sensitivity, and specificity to alternative high-throughput aligners bowtie2 [2], bwa [3], smalt, [4] GSNAP [5], and BLASR [6].

  4. HAMSA: Highly Accelerated Multiple Sequence Aligner

    Directory of Open Access Journals (Sweden)

    Naglaa M. Reda

    2016-06-01

    Full Text Available For biologists, the existence of an efficient tool for multiple sequence alignment is essential. This work presents a new parallel aligner called HAMSA. HAMSA is a bioinformatics application designed for highly accelerated alignment of multiple sequences of proteins and DNA/RNA on a multi-core cluster system. The design of HAMSA is based on a combination of our new optimized algorithms proposed recently of vectorization, partitioning, and scheduling. It mainly operates on a distance vector instead of a distance matrix. It accomplishes similarity computations and generates the guide tree in a highly accelerated and accurate manner. HAMSA outperforms MSAProbs with 21.9- fold speedup, and ClustalW-MPI of 11-fold speedup. It can be considered as an essential tool for structure prediction, protein classification, motive finding and drug design studies.

  5. Alignment for CSR

    International Nuclear Information System (INIS)

    Cooled Storage Ring of Heavy Ion Research Facility in Lanzhou (HIRFL-CSR) belongs to China great scientific project in China. The alignment for it is very difficult because of very large area and very high accuracy. For the special case in HIRFL-CSR, some new methods and new instruments are used, including the construction of survey control network, the usage of laser tracker, and CSR alignment database system with applications developed to store and analyze data. The author describes the whole procedure of CSR alignment

  6. Galaxy alignments: An overview

    CERN Document Server

    Joachimi, Benjamin; Kitching, Thomas D; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Hoekstra, Henk; Kiessling, Alina; Kirk, Donnacha; Rassat, Anais

    2015-01-01

    The alignments between galaxies, their underlying matter structures, and the cosmic web constitute vital ingredients for a comprehensive understanding of gravity, the nature of matter, and structure formation in the Universe. We provide an overview on the state of the art in the study of these alignment processes and their observational signatures, aimed at a non-specialist audience. The development of the field over the past one hundred years is briefly reviewed. We also discuss the impact of galaxy alignments on measurements of weak gravitational lensing, and discuss avenues for making theoretical and observational progress over the coming decade.

  7. CSA: An efficient algorithm to improve circular DNA multiple alignment

    Directory of Open Access Journals (Sweden)

    Pereira Luísa

    2009-07-01

    Full Text Available Abstract Background The comparison of homologous sequences from different species is an essential approach to reconstruct the evolutionary history of species and of the genes they harbour in their genomes. Several complete mitochondrial and nuclear genomes are now available, increasing the importance of using multiple sequence alignment algorithms in comparative genomics. MtDNA has long been used in phylogenetic analysis and errors in the alignments can lead to errors in the interpretation of evolutionary information. Although a large number of multiple sequence alignment algorithms have been proposed to date, they all deal with linear DNA and cannot handle directly circular DNA. Researchers interested in aligning circular DNA sequences must first rotate them to the "right" place using an essentially manual process, before they can use multiple sequence alignment tools. Results In this paper we propose an efficient algorithm that identifies the most interesting region to cut circular genomes in order to improve phylogenetic analysis when using standard multiple sequence alignment algorithms. This algorithm identifies the largest chain of non-repeated longest subsequences common to a set of circular mitochondrial DNA sequences. All the sequences are then rotated and made linear for multiple alignment purposes. To evaluate the effectiveness of this new tool, three different sets of mitochondrial DNA sequences were considered. Other tests considering randomly rotated sequences were also performed. The software package Arlequin was used to evaluate the standard genetic measures of the alignments obtained with and without the use of the CSA algorithm with two well known multiple alignment algorithms, the CLUSTALW and the MAVID tools, and also the visualization tool SinicView. Conclusion The results show that a circularization and rotation pre-processing step significantly improves the efficiency of public available multiple sequence alignment

  8. Multiple Sequence Alignment using GA and NN

    Directory of Open Access Journals (Sweden)

    Shuting Wu

    2008-12-01

    Full Text Available Multiple sequence alignment (MSA is an important tool in biological analysis. However, it is difficult to solve this class of problems, due to their exponential complexity. This paper presents an algorithm combining the genetic algorithm and a self-organizing neural network for solution to MSA. This approach demonstrates improved performance in long DNA and RNA data sets exhibiting small similarity.

  9. Applications of JNI Technology in Desktop Search Tool%JNI技术在桌面搜索工具中的应用

    Institute of Scientific and Technical Information of China (English)

    周强; 乐小虬; 李曦

    2013-01-01

    DocFetcher is an excellent open source desktop search tool written in the Java language,the tool supports document formats such as PDF,Word and PowerPoint. DocFetcher is trimmed,writing the creation index and retrieval index program. E-pass was developed using Visual C++,in order to integrate DocFetcher with e-pass,need to use C programming language called Java technology (Java N-ative Interface,referred to as JNI) implementations. It first describes the JNI,then describes the part C of JNI program in the desktop search tool,is divided into three parts,creating Java virtual machine,creating index,retrieving index. It lists the main program code with detailed description. Now,the desktop search tool has applied in the e-pass 2. 5 full version,features using correctly,stable operation. U-sing JNI as a bridge of data exchange,will give great flexibility of software. C language can be entirely in case of its own advantages,in-tegrates software developed by Java language,greater scope to achieve software reuse.%  DocFetcher是一个用Java语言编写的优秀开源桌面搜索工具,该工具支持的文档格式有PDF、Word、PowerPoint等.作者对DocFetcher进行了剪裁,编写了创建索引和检索索引程序. e划通是用Visual C++开发的,为了在e划通中集成DocFetcher,就需要采用C语言调用Java的技术(Java Native Interface,简称JNI)来实现.文中首先介绍了JNI,接着对该桌面搜索工具JNI中C部分的程序进行了说明,分为三部分,即创建Java虚拟机、创建索引、检索索引,文中列出了主要的程序代码,并且进行了详细说明.现在,该桌面搜索工具应用在e划通2.5完全版中,功能使用正确,运行稳定.采用JNI作为数据交换的桥梁,会给软件的实现带来极大的灵活性. C语言可以在完全体现自身优势的情况下,整合Java语言开发的软件,更大范围地实现了软件重用.

  10. Tidal alignment of galaxies

    CERN Document Server

    Blazek, Jonathan; Seljak, Uroš

    2015-01-01

    We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact of smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between ...

  11. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G.Gomez

    Since September, the muon alignment system shifted from a mode of hardware installation and commissioning to operation and data taking. All three optical subsystems (Barrel, Endcap and Link alignment) have recorded data before, during and after CRAFT, at different magnetic fields and during ramps of the magnet. This first data taking experience has several interesting goals: •    study detector deformations and movements under the influence of the huge magnetic forces; •    study the stability of detector structures and of the alignment system over long periods, •    study geometry reproducibility at equal fields (specially at 0T and 3.8T); •    reconstruct B=0T geometry and compare to nominal/survey geometries; •    reconstruct B=3.8T geometry and provide DT and CSC alignment records for CMSSW. However, the main goal is to recons...

  12. Alignment and commissioning of the APS beamline front ends

    International Nuclear Information System (INIS)

    Fifteen out of forty initial beamline front ends have been installed in the storage-ring tunnel at the 7-GeV Advanced Photon Source (APS). For the front-end installation, a four-step alignment process was designed and consists of (1) prealigning the front-end components with support tables in the preassembly area, (2) installing the components with tables in the storage-ring tunnel and aligning relative to the APS global telescope survey network, (3) confirming the alignment using a tooling laser alignment system, and (4) performing adjustments with the synchrotron-radiation beam during commissioning. The laser alignment system and the prealignment database have been of great importance for the expedient maintenance of front-end components. These tools are very important to a large synchrotron radiation facility, such as the APS, since they make a quick alignment setup possible and minimize alignment time inside the tunnel. This paper will present the four-step alignment process, the laser alignment system, and discuss the alignment confirmation results. copyright 1996 American Institute of Physics

  13. SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

    Directory of Open Access Journals (Sweden)

    Matija Korpar

    Full Text Available In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases.

  14. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    S. Szillasi

    2013-01-01

    The CMS detector has been gradually opened and whenever a wheel became exposed the first operation was the removal of the MABs, the sensor structures of the Hardware Barrel Alignment System. By the last days of June all 36 MABs have arrived at the Alignment Lab at the ISR where, as part of the Alignment Upgrade Project, they are refurbished with new Survey target holders. Their electronic checkout is on the way and finally they will be recalibrated. During LS1 the alignment system will be upgraded in order to allow more precise reconstruction of the MB4 chambers in Sector 10 and Sector 4. This requires new sensor components, so called MiniMABs (pictured below), that have already been assembled and calibrated. Image 6: Calibrated MiniMABs are ready for installation For the track-based alignment, the systematic uncertainties of the algorithm are under scrutiny: this study will enable the production of an improved Monte Carlo misalignment scenario and to update alignment position errors eventually, crucial...

  15. ATLAS Muon Endcap Alignment

    CERN Document Server

    Bensinger, J R

    2005-01-01

    To align the endcap muon chambers of the ATLAS experiment, an optical grid is set up between aluminum “alignment bars” nested in each layer of chambers. Optical lines are made of laser diodes and CCD cameras that form an alignment grid. The alignment bars are self-aligning. They are then carefully measured using a large coordinate measuring machine (CMM). The subsequent shape changes of the bar are determined by calculations that are corrected by the readings of the internal monitors. The relationship between the bars is then established by a network of sensors that measure the bearing angle of light sources on the other parts of the system. The system is over-determined and the location and orientation of each bar is determined using a fitting program. Chambers are then referenced to the alignment grid using proximity sensors. This information is used to provide corrections to the nominal chamber positions before calculating track momentum. The performance of the system has been validated in a test beam ...

  16. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2012-01-01

      A new muon alignment has been produced for 2012 A+B data reconstruction. It uses the latest Tracker alignment and single-muon data samples to align both DTs and CSCs. Physics validation has been performed and shows a modest improvement in stand-alone muon momentum resolution in the barrel, where the alignment is essentially unchanged from the previous version. The reference-target track-based algorithm using only collision muons is employed for the first time to align the CSCs, and a substantial improvement in resolution is observed in the endcap and overlap regions for stand-alone muons. This new alignment is undergoing the approval process and is expected to be deployed as part of a new global tag in the beginning of December. The pT dependence of the φ-bias in curvature observed in Monte Carlo was traced to a relative vertical misalignment between the Tracker and barrel muon systems. Moving the barrel as a whole to match the Tracker cures this pT dependence, leaving only the &phi...

  17. Nimble Protein Sequence Alignment in Grid (NPSAG

    Directory of Open Access Journals (Sweden)

    K. Somasundaram

    2008-01-01

    Full Text Available In Bio-Informatics application, the analysis of protein sequence is a kind of computation driven science which has rapidly and quickly growing biological data. Also databases used in these applications are heterogeneous in nature and alignment of protein sequence using physical techniques is expensive, slow and results are not always guaranteed/accurate. So this application requires cross-platform, cost-effective and more computing power algorithm for sequence matching and searching a sequence in database. Grid is one of the most emerging technologies of cost effective computing paradigm for large class of data and compute intensive application which enables large-scale aggregation and sharing of computational data and other resources across institutional boundaries. We proposed the Grid architecture for searching of distributed, heterogeneous genomic databases which contained protein sequences to speed up the analysis of large scale sequence data and performed sequence alignment for residues match.

  18. Structure alignment based on coding of local geometric measures

    Directory of Open Access Journals (Sweden)

    Rinne Andrew W

    2006-07-01

    quality structure alignments to be generated using standard algorithms of sequence alignment. This approach provides computationally efficient algorithms that allow fast database searching and multiple structure alignment. Because the geometric measure can employ different window sizes, the method allows the exploration of alignments on different, well-defined length scales.

  19. Automatic face alignment by maximizing similarity score

    OpenAIRE

    Boom, Bas; Spreeuwers, Luuk; Veldhuis, Raymond; Fred, A.; Jain, A. K.

    2007-01-01

    Accurate face registration is of vital importance to the performance of a face recognition algorithm. We propose a face registration method which searches for the optimal alignment by maximizing the score of a face recognition algorithm. In this paper we investigate the practical usability of our face registration method. Experiments show that our registration method achieves better results in face verification than the landmark based registration method. We even obtain face verification resu...

  20. Fine-tuning structural RNA alignments in the twilight zone

    Directory of Open Access Journals (Sweden)

    Schirmer Stefanie

    2010-04-01

    Full Text Available Abstract Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.

  1. Curriculum Alignment Research Suggests that Alignment Can Improve Student Achievement

    Science.gov (United States)

    Squires, David

    2012-01-01

    Curriculum alignment research has developed showing the relationship among three alignment categories: the taught curriculum, the tested curriculum and the written curriculum. Each pair (for example, the taught and the written curriculum) shows a positive impact for aligning those results. Following this, alignment results from the Third…

  2. MaxAlign: maximizing usable data in an alignment

    OpenAIRE

    Pedersen Anders G; Sackett Peter W; Gouveia-Oliveira Rodrigo

    2007-01-01

    Abstract Background The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. Results MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns – the alignment area – by selecting the ...

  3. Ergodic Secret Alignment

    CERN Document Server

    Bassily, Raef

    2010-01-01

    In this paper, we introduce two new achievable schemes for the fading multiple access wiretap channel (MAC-WT). In the model that we consider, we assume that perfect knowledge of the state of all channels is available at all the nodes in a causal fashion. Our schemes use this knowledge together with the time varying nature of the channel model to align the interference from different users at the eavesdropper perfectly in a one-dimensional space while creating a higher dimensionality space for the interfering signals at the legitimate receiver hence allowing for better chance of recovery. While we achieve this alignment through signal scaling at the transmitters in our first scheme (scaling based alignment (SBA)), we let nature provide this alignment through the ergodicity of the channel coefficients in the second scheme (ergodic secret alignment (ESA)). For each scheme, we obtain the resulting achievable secrecy rate region. We show that the secrecy rates achieved by both schemes scale with SNR as 1/2log(SNR...

  4. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez

    2010-01-01

    For the last three months, the Muon Alignment group has focussed on providing a new, improved set of alignment constants for the end-of-year data reprocessing. These constants were delivered on time and approved by the CMS physics validation team on November 17. The new alignment incorporates several improvements over the previous one from March for nearly all sub-systems. Motivated by the loss of information from a hardware failure in May (an entire MAB was lost), the optical barrel alignment has moved from a modular, super-plane reconstruction, to a full, single loop calculation of the entire geometry for all DTs in stations 1, 2 and 3. This makes better use of the system redundancy, mitigating the effect of the information loss. Station 4 is factorised and added afterwards to make the system smaller (and therefore faster to run), and also because the MAB calibration at the MB4 zone is less precise. This new alignment procedure was tested at 0 T against photogrammetry resulting in precisions of the order...

  5. Alignment telescope for Antares

    International Nuclear Information System (INIS)

    The Antares Automatic Alignment System employs a specially designed telescope for alignment of its laser beamlines. There are two telescopes in the system, and since each telescope is a primary alignment reference, stringent boresight accuracy and stability over the focus range were required. Optical and mechanical designs, which meet this requirement as well as that of image quality over a wide wavelength band, are described. Special test techniques for initial assembly and alignment of the telescope are also presented. The telescope, which has a 180-mm aperture FK51-KZF2 type glass doublet objective, requires a boresight accuracy of 2.8 μrad at two focal lengths, and object distances between 11 meters and infinity. Travel of a smaller secondary doublet provides focus from 11 m to infinity with approximately 7.8 m effective focal length. By flipping in a third doublet, the effective focal length is reduced to 2.5 m. Telescope alignment was accomplished by using a rotary air bearing to establish an axis in front of the system and placing the focus of a Laser Unequal Path Interferometer (LUPI) at the image plane

  6. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    Gervasio Gomez

    2012-01-01

      The new alignment for the DT chambers has been successfully used in physics analysis starting with the 52X Global Tag. The remaining main areas of development over the next few months will be preparing a new track-based CSC alignment and producing realistic APEs (alignment position errors) and MC misalignment scenarios to match the latest muon alignment constants. Work on these items has been delayed from the intended timeline, mostly due to a large involvement of the muon alignment man-power in physics analyses over the first half of this year. As CMS keeps probing higher and higher energies, special attention must be paid to the reconstruction of very-high-energy muons. Recent muon POG reports from mid-June show a φ-dependence in curvature bias in Monte Carlo samples. This bias is observed already at the tracker level, where it is constant with muon pT, while it grows with pT as muon chamber information is added to the tracks. Similar studies show a much smaller effect in data, at le...

  7. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    M. Dallavalle

    2013-01-01

    A new Muon misalignment scenario for 2011 (7 TeV) Monte Carlo re-processing was re-leased. The scenario is based on running of standard track-based reference-target algorithm (exactly as in data) using single-muon simulated sample (with the transverse-momentum spectrum matching data). It used statistics similar to what was used for alignment with 2011 data, starting from an initially misaligned Muon geometry from uncertainties of hardware measurements and using the latest Tracker misalignment geometry. Validation of the scenario (with muons from Z decay and high-pT simulated muons) shows that it describes data well. The study of systematic uncertainties (dominant by now due to huge amount of data collected by CMS and used for muon alignment) is finalised. Realistic alignment position errors are being obtained from the estimated uncertainties and are expected to improve the muon reconstruction performance. Concerning the Hardware Alignment System, the upgrade of the Barrel Alignment is in progress. By now, d...

  8. The CMS Tracker Alignment Strategy

    CERN Document Server

    Weber, Martin

    2006-01-01

    CMS silicon Tracker alignment consists of three key components: Survey during tracker construction, measurements with the Laser Alignment System during operation and track based alignment. Methods and results are explained in detail, with a special focus on track based alignment due to its enormous complexity and numerical challenges.

  9. RNA Structural Alignments, Part I

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Gorodkin, Jan

    Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...

  10. Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods

    OpenAIRE

    Muhammad Tariq Pervez; Masroor Ellahi Babar; Asif Nadeem; Muhammad Aslam; Ali Raza Awan; Naeem Aslam; Tanveer Hussain; Nasir Naveed; Salman Qadri; Usman Waheed; Muhammad Shoaib

    2014-01-01

    A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algorithm of each tool. Based on 10 simulated trees of different number of taxa generated by R, 400 known alignments and sequence files were constructed using indel-Seq-Gen. A total of 4000 test alignments were gen...

  11. Strategic Alignment of Business Intelligence

    OpenAIRE

    Cederberg, Niclas

    2010-01-01

    This thesis is about the concept of strategic alignment of business intelligence. It is based on a theoretical foundation that is used to define and explain business intelligence, data warehousing and strategic alignment. By combining a number of different methods for strategic alignment a framework for alignment of business intelligence is suggested. This framework addresses all different aspects of business intelligence identified as relevant for strategic alignment of business intelligence...

  12. RHIC survey and alignment

    International Nuclear Information System (INIS)

    The Relativistic Heavy Ion Collider consists of two interlaced plane rings, a pair of mirror-symmetric beam injection arcs, a spatially curved beam transfer line from the Alternating Gradient Synchrotron, and a collection of precisely positioned and aligned magnets, on appropriately positioned support stands, threaded on those arcs. RHIC geometry is defined by six beam crossing points exactly in a plane, lying precisely at the vertices of a regular hexagon of specified size position and orientation of this hexagon are defined geodetically. Survey control and alignment procedures, currently in use to construct RHIC, are described

  13. Local Structural Alignment of RNA with Affine Gap Model

    Science.gov (United States)

    Wong, Thomas K. F.; Cheung, Brenda W. Y.; Lam, T. W.; Yiu, S. M.

    Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.

  14. Image correlation method for DNA sequence alignment.

    Directory of Open Access Journals (Sweden)

    Millaray Curilem Saldías

    Full Text Available The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs and 100 scenes represented by 100 x 100 images each (in total, one million base pair database were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%, specificity (98.99% and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.

  15. Discriminative Shape Alignment

    DEFF Research Database (Denmark)

    Loog, M.; de Bruijne, M.

    taking into account that eventually the shapes are to be assigned to two or more different classes. This work introduces a discriminative variation to well-known Procrustes alignment and demonstrates its benefit over this classical method in shape classification tasks. The focus is on two...

  16. MUON DETECTORS: ALIGNMENT

    CERN Multimedia

    G. Gomez and Y. Pakhotin

    2012-01-01

      A new track-based alignment for the DT chambers is ready for deployment: an offline tag has already been produced which will become part of the 52X Global Tag. This alignment was validated within the muon alignment group both at low and high momentum using a W/Z skim sample. It shows an improved mass resolution for pairs of stand-alone muons, improved curvature resolution at high momentum, and improved DT segment extrapolation residuals. The validation workflow for high-momentum muons used to depend solely on the “split cosmics” method, looking at the curvature difference between muon tracks reconstructed in the upper or lower half of CMS. The validation has now been extended to include energetic muons decaying from heavily boosted Zs: the di-muon invariant mass for global and stand-alone muons is reconstructed, and the invariant mass resolution is compared for different alignments. The main areas of development over the next few months will be preparing a new track-based C...

  17. Aligning Mental Representations

    DEFF Research Database (Denmark)

    Kano Glückstad, Fumiko

    2013-01-01

    This work introduces a framework that implements asymmetric communication theory proposed by Sperber and Wilson [1]. The framework applies a generalization model known as the Bayesian model of generalization (BMG) [2] for aligning knowledge possessed by two communicating parties. The work focuses...

  18. Search and Disrupt

    OpenAIRE

    Ørding Olsen, Anders

    2015-01-01

    This paper analyzes how external search is affected by strategic interest alignment among knowledge sources. I focus on misalignment arising from the heterogeneous effects of disruptive technologies by analyzing the influence of incumbents on 2,855 non-incumbents? external knowledge search efforts. The efforts most likely to solve innovation problems obtained funding from the European Commission?s 7th Framework Program (2007-2013). The results show that involving incumbents improv...

  19. Alignment analysis of urban railways based on passenger travel demand

    DEFF Research Database (Denmark)

    Andersen, Jonas Lohmann Elkjær; Landex, Alex

    2010-01-01

    , this article presents a computerised GIS based methodology that can be used as decision support for selecting the best alignment. The methodology calculates travel potential within defined buffers surrounding the alignment. The methodology has three different approaches depending on the desired level of detail......: the simple but straight-forward to implement line potential approach that perform corridor analysis, the detailed catchment area analysis based on stops on the alignment and the refined service area analysis that uses search distances in street networks. All three approaches produce trustworthy results...

  20. Automatic generation of alignments for 3D QSAR analyses

    OpenAIRE

    Jewell, N.E.; D.B. Turner; Willett, P.; Sexton, G.J.

    2001-01-01

    Many 3D QSAR methods require the alignment of the molecules in a dataset, which can require a fair amount of manual effort in deciding upon a rational basis for the superposition. This paper describes the use of FBSS, a pro-ram for field-based similarity searching in chemical databases, for generating such alignments automatically. The CoMFA and CoMSIA experiments with several literature datasets show that the QSAR models resulting from the FBSS alignments are broadly comparable in predictive...

  1. Accelerating large-scale protein structure alignments with graphics processing units

    Directory of Open Access Journals (Sweden)

    Pang Bin

    2012-02-01

    Full Text Available Abstract Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs. As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU.

  2. [Advanced online search techniques and dedicated search engines for physicians].

    Science.gov (United States)

    Nahum, Yoav

    2008-02-01

    In recent years search engines have become an essential tool in the work of physicians. This article will review advanced search techniques from the world of information specialists, as well as some advanced search engine operators that may help physicians improve their online search capabilities, and maximize the yield of their searches. This article also reviews popular dedicated scientific and biomedical literature search engines. PMID:18357673

  3. MaxAlign: maximizing usable data in an alignment

    Directory of Open Access Journals (Sweden)

    Pedersen Anders G

    2007-08-01

    Full Text Available Abstract Background The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. Results MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid symbols that are present in gap-free columns – the alignment area – by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS that we consider useful for comparing tree topologies. Conclusion We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

  4. Avalanche for shape and feature-based virtual screening with 3D alignment.

    Science.gov (United States)

    Diller, David J; Connell, Nancy D; Welsh, William J

    2015-11-01

    This report introduces a new ligand-based virtual screening tool called Avalanche that incorporates both shape- and feature-based comparison with three-dimensional (3D) alignment between the query molecule and test compounds residing in a chemical database. Avalanche proceeds in two steps. The first step is an extremely rapid shape/feature based comparison which is used to narrow the focus from potentially millions or billions of candidate molecules and conformations to a more manageable number that are then passed to the second step. The second step is a detailed yet still rapid 3D alignment of the remaining candidate conformations to the query conformation. Using the 3D alignment, these remaining candidate conformations are scored, re-ranked and presented to the user as the top hits for further visualization and evaluation. To provide further insight into the method, the results from two prospective virtual screens are presented which show the ability of Avalanche to identify hits from chemical databases that would likely be missed by common substructure-based or fingerprint-based search methods. The Avalanche method is extended to enable patent landscaping, i.e., structural refinements to improve the patentability of hits for deployment in drug discovery campaigns. PMID:26458937

  5. Jet activity versus alignment

    CERN Document Server

    Lokhtin, I P; Sarycheva, L I; Snigirev, A M

    2005-01-01

    The hypothesis about the relation between the observed alignment of spots in the x-ray film in cosmic ray emulsion experiments and the features of events in which jets prevail at super high energies is tested. Due to strong correlation between jet axis directions and that between momenta (almost collinearity) of jet particles, the evaluated degree of alignment is considerably larger than that at randomly selected chaoticly located spots in the x-ray film. It appears comparable with experimental data provided that the height of primary interaction, the collision energy and the total energy of selected clusters meet certain conditions. The Monte Carlo generator PYTHIA, which basically well describes jet events in hadron-hadron interactions, was used for the analysis.

  6. Inflation by alignment

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, C.P. [PH -TH Division, CERN,CH-1211, Genève 23 (Switzerland); Department of Physics & Astronomy, McMaster University,1280 Main Street West, Hamilton ON (Canada); Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo ON (Canada); Roest, Diederik [Van Swinderen Institute for Particle Physics and Gravity, University of Groningen,Nijenborgh 4, 9747 AG Groningen (Netherlands)

    2015-06-08

    Pseudo-Goldstone bosons (pGBs) can provide technically natural inflatons, as has been comparatively well-explored in the simplest axion examples. Although inflationary success requires trans-Planckian decay constants, f≳M{sub p}, several mechanisms have been proposed to obtain this, relying on (mis-)alignments between potential and kinetic energies in multiple-field models. We extend these mechanisms to a broader class of inflationary models, including in particular the exponential potentials that arise for pGB potentials based on noncompact groups (and so which might apply to moduli in an extra-dimensional setting). The resulting potentials provide natural large-field inflationary models and can predict a larger primordial tensor signal than is true for simpler single-field versions of these models. In so doing we provide a unified treatment of several alignment mechanisms, showing how each emerges as a limit of the more general setup.

  7. Alignments of RNA structures.

    Science.gov (United States)

    Blin, Guillaume; Denise, Alain; Dulucq, Serge; Herrbach, Claire; Touzet, Hélène

    2010-01-01

    We describe a theoretical unifying framework to express the comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences for arc-annotated sequences and encompasses the main existing models for RNA structure comparison based on trees and arc-annotated sequences with a variety of edit operations. It also gives rise to edit models that have not been studied yet. We provide a thorough analysis of the alignment hierarchy, including a new polynomial-time algorithm and an NP-completeness proof. The polynomial-time algorithm involves biologically relevant edit operations such as pairing or unpairing nucleotides. It has been implemented in a software, called gardenia, which is available at the Web server http://bioinfo.lifl.fr/RNA/gardenia. PMID:20431150

  8. Improving Multiple Sequence Alignments by Revising Sequence Families with Alignment Scoring Approaches

    OpenAIRE

    Levchuk, Aleksandr O.

    2011-01-01

    Characterizing the functional, structural, and evolutionary relationships of biological sequences is an important task in modern genomics and computational biology. Most of these applications involve the assembly of sequence families by similarity searching, subsequent formation of multiple sequence alignments (MSAs) and downstream phylogenetic analyses. Especially, MSAs play a central role in this modeling workflow. Thus, the quality of the MSAs is of critical importance for its success. In ...

  9. Alignment of concerns

    DEFF Research Database (Denmark)

    Andersen, Tariq Osman; Bansler, Jørgen P.; Kensing, Finn; Moll, Jonas; Nielsen, Karen Dam

    E-health promises to enable and support active patient participation in chronic care. However, these fairly recent innovations are complicated matters and emphasize significant challenges, such as patients’ and clinicians’ different ways of conceptualizing disease and illness. Informed by insights...... from medical phenomenology and our own empirical work in telemonitoring and medical care of heart patients, we propose a design rationale for e-health systems conceptualized as the ‘alignment of concerns’....

  10. Nuclear reactor alignment plate configuration

    Science.gov (United States)

    Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R

    2014-01-28

    An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

  11. A rank-based sequence aligner with applications in phylogenetic analysis.

    Directory of Open Access Journals (Sweden)

    Liviu P Dinu

    Full Text Available Recent tools for aligning short DNA reads have been designed to optimize the trade-off between correctness and speed. This paper introduces a method for assigning a set of short DNA reads to a reference genome, under Local Rank Distance (LRD. The rank-based aligner proposed in this work aims to improve correctness over speed. However, some indexing strategies to speed up the aligner are also investigated. The LRD aligner is improved in terms of speed by storing [Formula: see text]-mer positions in a hash table for each read. Another improvement, that produces an approximate LRD aligner, is to consider only the positions in the reference that are likely to represent a good positional match of the read. The proposed aligner is evaluated and compared to other state of the art alignment tools in several experiments. A set of experiments are conducted to determine the precision and the recall of the proposed aligner, in the presence of contaminated reads. In another set of experiments, the proposed aligner is used to find the order, the family, or the species of a new (or unknown organism, given only a set of short Next-Generation Sequencing DNA reads. The empirical results show that the aligner proposed in this work is highly accurate from a biological point of view. Compared to the other evaluated tools, the LRD aligner has the important advantage of being very accurate even for a very low base coverage. Thus, the LRD aligner can be considered as a good alternative to standard alignment tools, especially when the accuracy of the aligner is of high importance. Source code and UNIX binaries of the aligner are freely available for future development and use at http://lrd.herokuapp.com/aligners. The software is implemented in C++ and Java, being supported on UNIX and MS Windows.

  12. Seeking the perfect alignment

    CERN Multimedia

    2002-01-01

    The first full-scale tests of the ATLAS Muon Spectrometer are about to begin in Prévessin. The set-up includes several layers of Monitored Drift Tubes Chambers (MDTs) and will allow tests of the performance of the detectors and of their highly accurate alignment system.   Monitored Drift Chambers in Building 887 in Prévessin, where they are just about to be tested. Muon chambers are keeping the ATLAS Muon Spectrometer team quite busy this summer. Now that most people go on holiday, the beam and alignment tests for these chambers are just starting. These chambers will measure with high accuracy the momentum of high-energy muons, and this implies very demanding requirements for their alignment. The MDT chambers consist of drift tubes, which are gas-filled metal tubes, 3 cm in diameter, with wires running down their axes. With high voltage between the wire and the tube wall, the ionisation due to traversing muons is detected as electrical pulses. With careful timing of the pulses, the position of the muon t...

  13. Alignment at the ESRF

    International Nuclear Information System (INIS)

    The ESRF Survey and Alignment group is responsible for the installation, control and periodic realignment of the accelerators and experiments which produce high quality x-rays used by scientists from Europe and around the world. Alignment tolerances are typically less than one millimetre and often in the order of several micrometers. The group is composed of one engineer, five highly trained survey technicians, one electronic and one computer technician. This team is fortified during peak periods by technicians from an external survey company. First an overview and comparative study of the main large-scale survey instrumentation and methods used by the group is made. Secondly a discussion of long term deformation on the ESRF site is presented. This is followed by presentation of the methods used in the realignment of the various machines. Two important aspects of our work, beamline and front-end alignment, and the so-called machine exotic devices are briefly discussed. Finally, the ESRF calibration bench is presented. (authors)

  14. Multiple sequence alignment accuracy and evolutionary distance estimation

    Directory of Open Access Journals (Sweden)

    Rosenberg Michael S

    2005-11-01

    Full Text Available Abstract Background Sequence alignment is a common tool in bioinformatics and comparative genomics. It is generally assumed that multiple sequence alignment yields better results than pair wise sequence alignment, but this assumption has rarely been tested, and never with the control provided by simulation analysis. This study used sequence simulation to examine the gain in accuracy of adding a third sequence to a pair wise alignment, particularly concentrating on how the phylogenetic position of the additional sequence relative to the first pair changes the accuracy of the initial pair's alignment as well as their estimated evolutionary distance. Results The maximal gain in alignment accuracy was found not when the third sequence is directly intermediate between the initial two sequences, but rather when it perfectly subdivides the branch leading from the root of the tree to one of the original sequences (making it half as close to one sequence as the other. Evolutionary distance estimation in the multiple alignment framework, however, is largely unrelated to alignment accuracy and rather is dependent on the position of the third sequence; the closer the branch leading to the third sequence is to the root of the tree, the larger the estimated distance between the first two sequences. Conclusion The bias in distance estimation appears to be a direct result of the standard greedy progressive algorithm used by many multiple alignment methods. These results have implications for choosing new taxa and genomes to sequence when resources are limited.

  15. Alignment as a Teacher Variable

    Science.gov (United States)

    Porter, Andrew C.; Smithson, John; Blank, Rolf; Zeidner, Timothy

    2007-01-01

    With the exception of the procedures developed by Porter and colleagues (Porter, 2002), other methods of defining and measuring alignment are essentially limited to alignment between tests and standards. Porter's procedures have been generalized to investigating the alignment between content standards, tests, textbooks, and even classroom…

  16. Improving your target-template alignment with MODalign.

    KAUST Repository

    Barbato, Alessandro

    2012-02-04

    SUMMARY: MODalign is an interactive web-based tool aimed at helping protein structure modelers to inspect and manually modify the alignment between the sequences of a target protein and of its template(s). It interactively computes, displays and, upon modification of the target-template alignment, updates the multiple sequence alignments of the two protein families, their conservation score, secondary structure and solvent accessibility values, and local quality scores of the implied three-dimensional model(s). Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all cases where a sequence alignment needs to be inspected in the context of other biological information. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://modorama.biocomputing.it/modalign. Website implemented in HTML and JavaScript with all major browsers supported. CONTACT: jan.kosinski@uniroma1.it.

  17. 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.

  18. The CMS Muon System Alignment

    CERN Document Server

    Martinez Ruiz-Del-Arbol, P

    2009-01-01

    The alignment of the muon system of CMS is performed using different techniques: photogrammetry measurements, optical alignment and alignment with tracks. For track-based alignment, several methods are employed, ranging from a hit and impact point (HIP) algorithm and a procedure exploiting chamber overlaps to a global fit method based on the Millepede approach. For start-up alignment as long as available integrated luminosity is still significantly limiting the size of the muon sample from collisions, cosmic muon and beam halo signatures play a very strong role. During the last commissioning runs in 2008 the first aligned geometries have been produced and validated with data. The CMS offline computing infrastructure has been used in order to perform improved reconstructions. We present the computational aspects related to the calculation of alignment constants at the CERN Analysis Facility (CAF), the production and population of databases and the validation and performance in the official reconstruction. Also...

  19. Beam alignment system

    International Nuclear Information System (INIS)

    A patent is claimed for the invention of a beam alignment system. The aim of the invention is the obtention of an accurate monitoring of the beam position and direction. It is of great interest in the nuclear industry. The invention can be applied in an infrared laser beam for welding operations. An auxiliar radiation source is incorporated to the device. The system's configuration allows a simultaneous and separated utilisation of two beams. The description and the design of the proposed system are provided

  20. Alignment in hadronic interactions

    CERN Document Server

    Wibig, T

    2000-01-01

    The alignment of the products of very high energy interactions seen in mountain altitude experiments is one of the most puzzling phenomena in cosmic ray physics for quite a long time. The observations of the Pamir and Chacaltaya emulsion chamber groups and by the Tien-Shan extensive air shower experiment, together with a very clear event seen in the Concorde French-Japanese experiment in the stratosphere, makes the experimental basis very substantial. In the present paper a novel possible explanation is put forward.

  1. Searches for standard model Higgs boson and supersymmetry - Trigger studies and software tools development for new phenomena in the DO experiment

    International Nuclear Information System (INIS)

    This document presents a summary of my research work during the past 7 years for the preparation of the D0 experiment at Fermilab and the analysis of the data collected at the Tevatron hadron collider. It mainly focuses on 2 topics: trigger and direct search for new phenomena, particularly on supersymmetry and standard model Higgs boson searches. This document is divided into 5 chapters: 1) the phenomenology of the standard model and beyond, 2) the phenomenology of pp-bar events, 3) the Tevatron and D0 detector, 4) the trigger system and data acquisition, and 5) data analysis: search for supersymmetry and Higgs boson

  2. LASAGNA: A novel algorithm for transcription factor binding site alignment

    OpenAIRE

    Lee, Chih; Huang, Chun-Hsi

    2013-01-01

    Background Scientists routinely scan DNA sequences for transcription factor (TF) binding sites (TFBSs). Most of the available tools rely on position-specific scoring matrices (PSSMs) constructed from aligned binding sites. Because of the resolutions of assays used to obtain TFBSs, databases such as TRANSFAC, ORegAnno and PAZAR store unaligned variable-length DNA segments containing binding sites of a TF. These DNA segments need to be aligned to build a PSSM. While the TRANSFAC database provid...

  3. Create powerful Broader Impact Tools and k-16 inquiry lessons aligned to next generation standards for this generation of science students by building a partnership between scientists and educational coordinators

    Science.gov (United States)

    Cohen, E.; Quan, T. M.

    2012-12-01

    A model of collaboration between research scientists, educational non-profit organizations and practicing classroom teachers will be explained. This method can provide a researcher with support providing educationally sound age appropriate science lessons while doing what they love most, researching! Appointing an educational coordinator to fulfill broader impacts may sound out of the ordinary, but evaluators recognize the important aspect of finding experts to support research in the Broader Impact, just as you would in the science part of the grant. By creating a team using experts in their field, the scientist can focus on the science while the broader Impacts will impact students and teachers. There was a team made out of experts, research, and data from the International Ocean Drilling Program, Oklahoma State University, Rutgers, and public school teachers. The educational coordinator aligns the high end scientific work to standards and benchmark for each group of students. Once the content is academically leveled at age appropriate readiness, successful lessons can be created. The scientists provide content and the non-profits provide facilitation and a way to implement the lessons created over a national scope.

  4. Search and Disrupt

    DEFF Research Database (Denmark)

    Ørding Olsen, Anders

    This paper analyzes how external search is affected by strategic interest alignment among knowledge sources. I focus on misalignment arising from the heterogeneous effects of disruptive technologies by analyzing the influence of incumbents on 2,855 non-incumbents? external knowledge search efforts....... The efforts most likely to solve innovation problems obtained funding from the European Commission?s 7th Framework Program (2007-2013). The results show that involving incumbents improves search in complementary technologies, while demoting it when strategic interests are misaligned in disruptive...... technologies. However, incumbent sources engaged in capability reconfiguration to accommodate disruption improve search efforts in disruptive technologies. The paper concludes that the value of external sources is contingent on more than their knowledge. Specifically, interdependence of sources in search gives...

  5. All about alignment

    CERN Multimedia

    2006-01-01

    The ALICE absorbers, iron wall and superstructure have been installed with great precision. The ALICE front absorber, positioned in the centre of the detector, has been installed and aligned. Weighing more than 400 tonnes, the ALICE absorbers and the surrounding support structures have been installed and aligned with a precision of 1-2 mm, hardly an easy task but a very important one. The ALICE absorbers are made of three parts: the front absorber, a 35-tonne cone-shaped structure, and two small-angle absorbers, long straight cylinder sections weighing 18 and 40 tonnes. The three pieces lined up have a total length of about 17 m. In addition to these, ALICE technicians have installed a 300-tonne iron filter wall made of blocks that fit together like large Lego pieces and a surrounding metal support structure to hold the tracking and trigger chambers. The absorbers house the vacuum chamber and are also the reference surface for the positioning of the tracking and trigger chambers. For this reason, the ab...

  6. Computing alignment plots efficiently

    CERN Document Server

    Krusche, Peter

    2009-01-01

    Dot plots are a standard method for local comparison of biological sequences. In a dot plot, a substring to substring distance is computed for all pairs of fixed-size windows in the input strings. Commonly, the Hamming distance is used since it can be computed in linear time. However, the Hamming distance is a rather crude measure of string similarity, and using an alignment-based edit distance can greatly improve the sensitivity of the dot plot method. In this paper, we show how to compute alignment plots of the latter type efficiently. Given two strings of length m and n and a window size w, this problem consists in computing the edit distance between all pairs of substrings of length w, one from each input string. The problem can be solved by repeated application of the standard dynamic programming algorithm in time O(mnw^2). This paper gives an improved data-parallel algorithm, running in time $O(mnw/\\gamma/p)$ using vector operations that work on $\\gamma$ values in parallel and $p$ processors. We show ex...

  7. Conditional alignment random fields for multiple motion sequence alignment.

    Science.gov (United States)

    Kim, Minyoung

    2013-11-01

    We consider the multiple time-series alignment problem, typically focusing on the task of synchronizing multiple motion videos of the same kind of human activity. Finding an optimal global alignment of multiple sequences is infeasible, while there have been several approximate solutions, including iterative pairwise warping algorithms and variants of hidden Markov models. In this paper, we propose a novel probabilistic model that represents the conditional densities of the latent target sequences which are aligned with the given observed sequences through the hidden alignment variables. By imposing certain constraints on the target sequences at the learning stage, we have a sensible model for multiple alignments that can be learned very efficiently by the EM algorithm. Compared to existing methods, our approach yields more accurate alignment while being more robust to local optima and initial configurations. We demonstrate its efficacy on both synthetic and real-world motion videos including facial emotions and human activities. PMID:24051737

  8. DatAlign - implementation of the new APS survey and alignment database

    International Nuclear Information System (INIS)

    The Advanced Photon Source (APS) at Argonne National Laboratory is a national 3rd-generation synchrotron-radiation light source research facility located about twenty-five miles southwest of Chicago. The APS accelerator systems and X-ray beamlines are approximately six kilometers in length with more than four thousand precisely aligned components. The APS Survey and Alignment Group (SAG) is responsible for the correct positioning of beamline components for the APS accelerator systems. SAG fiducializes beamline components, aligns components in the accelerator tunnel and in the experiment hall, and maintains all necessary geodetic control networks to achieve required placement tolerances. All these tasks generate large amounts of data that have to be stored and readily accessible to the SAG members. As a result, the utilization of a database system is inevitable. During the 1990s, the SAG depended on Geonet software (1) for its data storage and management needs. Geonet was originally developed under the DOS environment at SLAC in the 1980s as an all-inclusive software package for the accelerator alignment community. After a decade of a reliable service, Geonet unavoidably became obsolete. First, some Geonet utilities, like data collection and data reduction programs, were phased out or replaced by new tools to keep up with advancements in survey and alignment technology. By the year 2002, a decision was made to also replace the database portion of Geonet with a new relational database. The conceptual design of the new APS Survey and Alignment Database (2) was completed in 2002. After a review of commercially available database management systems (DBMSs), Microsoft(regsign) Access 2000 was chosen for the implementation of our database design. The implementation of the new database (DB), under the name 'DatAlign,' commenced the following year.

  9. Word-aligned parallel text : a new resource for contrastive language studies

    OpenAIRE

    Volk, Martin; Göhring, Anne; Lehner, Stéphanie; Rios, Annette; Sennrich, Rico; Uibo, Heli

    2011-01-01

    This paper describes the opportunities that arise from automatic word alignment for bilingual concordances and contrastive language studies. We introduce our parallel corpus of Alpine texts in French and German and our web-based alignment search system. We explain how we have reduced the number of erroneous alignments in the output by distinguishing between dominant and miscellaneous translations. We are currently in the process of extending the system to a new language pair Spanish-Quechua. ...

  10. Alignment procedures for the CMS silicon tracker

    CERN Document Server

    Behr, Joerg

    2012-01-01

    The CMS all-silicon tracker consists of 16588 modules. Therefore its alignment procedures require sophisticated algorithms. Advanced tools of computing, tracking and data analysis have been deployed for reaching the targeted performance. Ultimate local precision is now achieved by the determination of sensor curvatures, challenging the algorithms to determine about 200k parameters simultaneously. Systematic biases in the geometry are controlled by adding further information into the alignment workflow, e.g. the mass of decaying resonances. The orientation of the tracker with respect to the magnetic field of CMS is determined with a stand-alone chi-square minimization procedure. The geometries are finally carefully validated. The monitored quantities include the basic track quantities for tracks from both collisions and cosmic muons and physics observables.

  11. Alignment procedures for the CMS silicon tracker

    International Nuclear Information System (INIS)

    The CMS all-silicon tracker consists of 16588 modules. Therefore its alignment procedures require sophisticated algorithms. Advanced tools of computing, tracking and data analysis have been deployed for reaching the targeted performance. Ultimate local precision is now achieved by the determination of sensor curvatures, challenging the algorithms to determine about 200k parameters simultaneously. Systematic biases in the geometry are controlled by adding further information into the alignment workflow, e.g. the mass of decaying resonances. The orientation of the tracker with respect to the magnetic field of CMS is determined with a stand-alone chi-square minimization procedure. The geometries are finally carefully validated. The monitored quantities include the basic track quantities for tracks from both collisions and cosmic muons and physics observables.

  12. The surveyors' quest for perfect alignment

    CERN Multimedia

    2003-01-01

    Photogrammetry of a CMS endcap and part of the hadronic calorimeter.The structure was covered with targets photographed by digital cameras. Perfect alignment.... Although CERN's surveyors do not claim to achieve it, they are constantly striving for it and deploy all necessary means to come as close as they can. In their highly specialised field of large-scale metrology, the solution lies in geodesy and photogrammetry, both of which are based on increasingly sophisticated instruments and systems. In civil engineering, these techniques are used for non-destructive inspection of bridges, dams and other structures, while industrial applications include dimensional verification and deformation measurement in large mechanical assemblies. The same techniques also come into play for the metrology of research tools such as large telescopes and of course, particle accelerators. Particle physics laboratories are especially demanding customers, and CERN has often asked for the impossible. As a result, the alignment metro...

  13. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    Directory of Open Access Journals (Sweden)

    Arabi E. keshk

    2014-05-01

    Full Text Available The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between sequences. This paper introduces an enhancement of dynamic algorithm of genome sequence alignment, which called EDAGSA. It is filling the three main diagonals without filling the entire matrix by the unused data. It gets the optimal solution with decreasing the execution time and therefore the performance is increased. To illustrate the effectiveness of optimizing the performance of the proposed algorithm, it is compared with the traditional methods such as Needleman-Wunsch, Smith-Waterman and longest common subsequence algorithms. Also, database is implemented for using the algorithm in multi-sequence alignments for searching the optimal sequence that matches the given sequence.

  14. Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods

    Science.gov (United States)

    Pervez, Muhammad Tariq; Babar, Masroor Ellahi; Nadeem, Asif; Aslam, Muhammad; Awan, Ali Raza; Aslam, Naeem; Hussain, Tanveer; Naveed, Nasir; Qadri, Salman; Waheed, Usman; Shoaib, Muhammad

    2014-01-01

    A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algorithm of each tool. Based on 10 simulated trees of different number of taxa generated by R, 400 known alignments and sequence files were constructed using indel-Seq-Gen. A total of 4000 test alignments were generated to study the effect of sequence length, indel size, deletion rate, and insertion rate. Results showed that alignment quality was highly dependent on the number of deletions and insertions in the sequences and that the sequence length and indel size had a weaker effect. Overall, ProbCons was consistently on the top of list of the evaluated MSA tools. SATe, being little less accurate, was 529.10% faster than ProbCons and 236.72% faster than MAFFT(L-INS-i). Among other tools, Kalign and MUSCLE achieved the highest sum of pairs. We also considered BALiBASE benchmark datasets and the results relative to BAliBASE- and indel-Seq-Gen-generated alignments were consistent in the most cases. PMID:25574120

  15. Dust alignment in astrophysical environments

    Science.gov (United States)

    Lazarian, Alex; Thiem Hoang, Chi

    Dust is known to be aligned in interstellar medium and the arising polarization is extensively used to trace magnetic fields. What process aligns dust grains was one of the most long-standing problems of astrophysics in spite of the persistent efforts to solve it. For years the Davis-Greenstein paramagnetic alignment was the primary candidate for explaining grain alignment. However, the situation is different now and the most promising mechanism is associated with radiative torques (RATs) acting on irregular grains. I shall present the analytical theory of RAT alignment, discuss the observational tests that support this theory. I shall also discuss in what situations we expect to see the dominance of paramagnetic alignment.

  16. Nova laser alignment control system

    International Nuclear Information System (INIS)

    Alignment of the Nova laser requires control of hundreds of optical components in the ten beam paths. Extensive application of computer technology makes daily alignment practical. The control system is designed in a manner which provides both centralized and local manual operator controls integrated with automatic closed loop alignment. Menudriven operator consoles using high resolution color graphics displays overlaid with transport touch panels allow laser personnel to interact efficiently with the computer system. Automatic alignment is accomplished by using image analysis techniques to determine beam references points from video images acquired along the laser chain. A major goal of the design is to contribute substantially to rapid experimental turnaround and consistent alignment results. This paper describes the computer-based control structure and the software methods developed for aligning this large laser system

  17. Nuclear reactor internals alignment configuration

    Science.gov (United States)

    Gilmore, Charles B.; Singleton, Norman R.

    2009-11-10

    An alignment system that employs jacking block assemblies and alignment posts around the periphery of the top plate of a nuclear reactor lower internals core shroud to align an upper core plate with the lower internals and the core shroud with the core barrel. The distal ends of the alignment posts are chamfered and are closely received within notches machined in the upper core plate at spaced locations around the outer circumference of the upper core plate. The jacking block assemblies are used to center the core shroud in the core barrel and the alignment posts assure the proper orientation of the upper core plate. The alignment posts may alternately be formed in the upper core plate and the notches may be formed in top plate.

  18. Improvement of Performance of MegaBlast Algorithm for DNA Sequence Alignment

    Institute of Scientific and Technical Information of China (English)

    Guang-Ming Tan; Lin Xu; Dong-Bo Bu; Sheng-Zhong Feng; Ning-Hui Sun

    2006-01-01

    MegaBlast is one of the most important programs in NCBI BLAST (Basic Local Alignment Search Tool)toolkits. However, MegaBlast is computation and I/O intensive. It consumes a great deal of memory which is proportional to the size of the query sequences set and subject (database) sequences set of product. This paper proposes a new strategy for optimizing MegaBlast. The new strategy exchanges the query and subject sequences sets, and builds a hash table based on new subject sequences. It overlaps I/O with computation, shortens the overall time and reduces the cost of memory,since the memory here is only proportional to the size of subject sequences set. The optimized algorithm is suitable to be parallelized in cluster systems. The parallel algorithm uses query segmentation method. As our experiments shown, the parallel program which is implemented with MPI has fine scalability.

  19. Catalyzing alignment processes

    DEFF Research Database (Denmark)

    Lauridsen, Erik Hagelskjær; Jørgensen, Ulrik

    2004-01-01

    time and in combination with other social processes establish more aligned and standardized environmental performance between countries. However, examples of the introduction of environmental management suggests that EMS’ only plays a minor role in developing the actual environmental objectives......This paper describes how environmental management systems (EMS) spur the circulation of processes that support the constitution of environmental issues as specific environ¬mental objects and objectives. EMS catalyzes alignmentprocesses that produce coherence among the different elements involved...... they are implemented in and how the changing context is reflected in the environmental objectives that are established and prioritised. Our argument is, that the ability of the standard to achieve an impact is dependant on the constitution of ’coherent’ environmental issues in the context, where the management system...

  20. On aligning trees

    CERN Document Server

    Calder, J

    1997-01-01

    The increasing availability of corpora annotated for linguistic structure prompts the question: if we have the same texts, annotated for phrase structure under two different schemes, to what extent do the annotations agree on structuring within the text? We suggest the term tree alignment to indicate the situation where two markup schemes choose to bracket off the same text elements. We propose a general method for determining agreement between two analyses. We then describe an efficient implementation, which is also modular in that the core of the implementation can be reused regardless of the format of markup used in the corpora. The output of the implementation on the Susanne and Penn treebank corpora is discussed.

  1. SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

    Directory of Open Access Journals (Sweden)

    Steven N Hart

    Full Text Available BACKGROUND: Structural variation (SV represents a significant, yet poorly understood contribution to an individual's genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. RESULTS: We developed and validated SoftSearch using real and synthetic datasets. SoftSearch's key features are 1 not requiring secondary (or exhaustive primary alignment, 2 portability into established sequencing workflows, and 3 is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.. SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. CONCLUSIONS: We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance.

  2. Peppy: Proteogenomic Search Software

    OpenAIRE

    Risk, Brian A.; Spitzer, Wendy J; Giddings, Morgan C

    2013-01-01

    Proteogenomic searching is a useful method for identifying novel proteins, annotating genes and detecting peptides unique to an individual genome. The approach, however, can be laborious, as it often requires search segmentation and the use of several unintegrated tools. Furthermore, many proteogenomic efforts have been limited to small genomes, as large genomes can prove impractical due to the required amount of computer memory and computation time. We present Peppy, a software tool designed...

  3. MaxAlign: maximizing usable data in an alignment

    DEFF Research Database (Denmark)

    Oliveira, Rodrigo Gouveia; Sackett, Peter Wad; Pedersen, Anders Gorm

    2007-01-01

    of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand...

  4. SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters

    Directory of Open Access Journals (Sweden)

    Lefkowitz Elliot J

    2004-10-01

    Full Text Available Abstract Background Large-scale sequence comparison is a powerful tool for biological inference in modern molecular biology. Comparing new sequences to those in annotated databases is a useful source of functional and structural information about these sequences. Using software such as the basic local alignment search tool (BLAST or HMMPFAM to identify statistically significant matches between newly sequenced segments of genetic material and those in databases is an important task for most molecular biologists. Searching algorithms are intrinsically slow and data-intensive, especially in light of the rapid growth of biological sequence databases due to the emergence of high throughput DNA sequencing techniques. Thus, traditional bioinformatics tools are impractical on PCs and even on dedicated UNIX servers. To take advantage of larger databases and more reliable methods, high performance computation becomes necessary. Results We describe the implementation of SS-Wrapper (Similarity Search Wrapper, a package of wrapper applications that can parallelize similarity search applications on a Linux cluster. Our wrapper utilizes a query segmentation-search (QS-search approach to parallelize sequence database search applications. It takes into consideration load balancing between each node on the cluster to maximize resource usage. QS-search is designed to wrap many different search tools, such as BLAST and HMMPFAM using the same interface. This implementation does not alter the original program, so newly obtained programs and program updates should be accommodated easily. Benchmark experiments using QS-search to optimize BLAST and HMMPFAM showed that QS-search accelerated the performance of these programs almost linearly in proportion to the number of CPUs used. We have also implemented a wrapper that utilizes a database segmentation approach (DS-BLAST that provides a complementary solution for BLAST searches when the database is too large to fit into

  5. Google - Security Testing Tool

    OpenAIRE

    Staykov, Georgi

    2007-01-01

    Using Google as a security testing tool, basic and advanced search techniques using advanced google search operators. Examples of obtaining control over security cameras, VoIP systems, web servers and collecting valuable information as: Credit card details, cvv codes – only using Google.

  6. Pyro-Align: Sample-Align based Multiple Alignment system for Pyrosequencing Reads of Large Number

    CERN Document Server

    Saeed, Fahad

    2009-01-01

    Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard and heuristics are designed for approximate solutions. Multiple sequence alignment of pyrosequenceing reads is complex mainly because of 2 factors. One being the huge number of reads, making the use of traditional heuristics,that scale very poorly for large number, unsuitable. The second reason is that the alignment cannot be performed arbitrarily, because the position of the reads with respect to the original genome is important and has to be taken into account.In this report we present a short description of the multiple alignment system for pyrosequencing reads.

  7. Mastering Search Analytics Measuring SEO, SEM and Site Search

    CERN Document Server

    Chaters, Brent

    2011-01-01

    Many companies still approach Search Engine Optimization (SEO) and paid search as separate initiatives. This in-depth guide shows you how to use these programs as part of a comprehensive strategy-not just to improve your site's search rankings, but to attract the right people and increase your conversion rate. Learn how to measure, test, analyze, and interpret all of your search data with a wide array of analytic tools. Gain the knowledge you need to determine the strategy's return on investment. Ideal for search specialists, webmasters, and search marketing managers, Mastering Search Analyt

  8. An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

    Directory of Open Access Journals (Sweden)

    Taneda Akito

    2008-12-01

    Full Text Available Abstract Background Aligning RNA sequences with low sequence identity has been a challenging problem since such a computation essentially needs an algorithm with high complexities for taking structural conservation into account. Although many sophisticated algorithms for the purpose have been proposed to date, further improvement in efficiency is necessary to accelerate its large-scale applications including non-coding RNA (ncRNA discovery. Results We developed a new genetic algorithm, Cofolga2, for simultaneously computing pairwise RNA sequence alignment and consensus folding, and benchmarked it using BRAliBase 2.1. The benchmark results showed that our new algorithm is accurate and efficient in both time and memory usage. Then, combining with the originally trained SVM, we applied the new algorithm to novel ncRNA discovery where we compared S. cerevisiae genome with six related genomes in a pairwise manner. By focusing our search to the relatively short regions (50 bp to 2,000 bp sandwiched by conserved sequences, we successfully predict 714 intergenic and 1,311 sense or antisense ncRNA candidates, which were found in the pairwise alignments with stable consensus secondary structure and low sequence identity (≤ 50%. By comparing with the previous predictions, we found that > 92% of the candidates is novel candidates. The estimated rate of false positives in the predicted candidates is 51%. Twenty-five percent of the intergenic candidates has supports for expression in cell, i.e. their genomic positions overlap those of the experimentally determined transcripts in literature. By manual inspection of the results, moreover, we obtained four multiple alignments with low sequence identity which reveal consensus structures shared by three species/sequences. Conclusion The present method gives an efficient tool complementary to sequence-alignment-based ncRNA finders.

  9. Autonomous Search

    CERN Document Server

    Hamadi, Youssef; Saubion, Frédéric

    2012-01-01

    Decades of innovations in combinatorial problem solving have produced better and more complex algorithms. These new methods are better since they can solve larger problems and address new application domains. They are also more complex which means that they are hard to reproduce and often harder to fine-tune to the peculiarities of a given problem. This last point has created a paradox where efficient tools are out of reach of practitioners. Autonomous search (AS) represents a new research field defined to precisely address the above challenge. Its major strength and originality consist in the

  10. Advanced Alignment of the ATLAS Tracking System

    CERN Document Server

    Butti, P; The ATLAS collaboration

    2014-01-01

    In order to reconstruct the trajectories of charged particles, the ATLAS experiment exploits a tracking system built using different technologies, planar silicon modules or microstrips (PIX and SCT detectors) and gaseous drift tubes (TRT), all embedded in a 2T solenoidal magnetic field. Misalignments and deformations of the active detector elements deteriorate the track reconstruction resolution and lead to systematic biases on the measured track parameters. The alignment procedures exploits various advanced tools and techniques in order to determine for module positions and correct for deformations. For the LHC Run II, the system is being upgraded with the installation of a new pixel layer, the Insertable B-layer (IBL).

  11. Protein structure search and local structure characterization

    Directory of Open Access Journals (Sweden)

    Ku Shih-Yen

    2008-08-01

    Full Text Available Abstract Background Structural similarities among proteins can provide valuable insight into their functional mechanisms and relationships. As the number of available three-dimensional (3D protein structures increases, a greater variety of studies can be conducted with increasing efficiency, among which is the design of protein structural alphabets. Structural alphabets allow us to characterize local structures of proteins and describe the global folding structure of a protein using a one-dimensional (1D sequence. Thus, 1D sequences can be used to identify structural similarities among proteins using standard sequence alignment tools such as BLAST or FASTA. Results We used self-organizing maps in combination with a minimum spanning tree algorithm to determine the optimum size of a structural alphabet and applied the k-means algorithm to group protein fragnts into clusters. The centroids of these clusters defined the structural alphabet. We also developed a flexible matrix training system to build a substitution matrix (TRISUM-169 for our alphabet. Based on FASTA and using TRISUM-169 as the substitution matrix, we developed the SA-FAST alignment tool. We compared the performance of SA-FAST with that of various search tools in database-scale search tasks and found that SA-FAST was highly competitive in all tests conducted. Further, we evaluated the performance of our structural alphabet in recognizing specific structural domains of EGF and EGF-like proteins. Our method successfully recovered more EGF sub-domains using our structural alphabet than when using other structural alphabets. SA-FAST can be found at http://140.113.166.178/safast/. Conclusion The goal of this project was two-fold. First, we wanted to introduce a modular design pipeline to those who have been working with structural alphabets. Secondly, we wanted to open the door to researchers who have done substantial work in biological sequences but have yet to enter the field of protein

  12. Lexical alignment in triadic communication

    Directory of Open Access Journals (Sweden)

    Anouschka eFoltz

    2015-02-01

    Full Text Available Lexical alignment refers to the adoption of one’s interlocutor’s lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants’ lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment.

  13. Faster and More Accurate Sequence Alignment with SNAP

    CERN Document Server

    Zaharia, Matei; Curtis, Kristal; Fox, Armando; Patterson, David; Shenker, Scott; Stoica, Ion; Karp, Richard M; Sittler, Taylor

    2011-01-01

    We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent aligners based on the Burrows-Wheeler transform, SNAP uses a simple hash index of short seed sequences from the genome, similar to BLAST's. However, SNAP greatly reduces the number and cost of local alignment checks performed through several measures: it uses longer seeds to reduce the false positive locations considered, leverages larger memory capacities to speed index lookup, and excludes most candidate locations without fully computing their edit distance to the read. The result is an algorithm that scales well for reads from one hundred to thousands of bases long and provides a rich error model that can match classes of mutations (e.g., longer indels) that today's fast aligners ignore. We calculate that SNAP can align a dataset with 30x coverage of a human genome in le...

  14. Alignments in the nobelium isotopes

    Institute of Scientific and Technical Information of China (English)

    ZHENG Shi-Zie; XU Fu-Rong; YUAN Cen-Xi; QI Chong

    2009-01-01

    Total-Routhian-Surface calculations have been performed to investigate the deformation and align-ment properties of the No isotopes. It is found that normal deformed and superdeformed states in these nuclei can coexist at low excitation energies. In neutron-deficient No isotopes, the superdeformed shapes can even become the ground states. Moreover, we plotted the kinematic moments of inertia of the No isotopes, which follow very nicely available experimental data. It is noted that, as the rotational frequency increases, align-ments develop at hω=0.2-0.3 MeV. Our calculations show that the occupation of the vj orbital plays an important role in the alignments of the No isotopes.

  15. The CMS Silicon Tracker Alignment

    CERN Document Server

    Castello, R

    2008-01-01

    The alignment of the Strip and Pixel Tracker of the Compact Muon Solenoid experiment, with its large number of independent silicon sensors and its excellent spatial resolution, is a complex and challenging task. Besides high precision mounting, survey measurements and the Laser Alignment System, track-based alignment is needed to reach the envisaged precision.\\\\ Three different algorithms for track-based alignment were successfully tested on a sample of cosmic-ray data collected at the Tracker Integration Facility, where 15\\% of the Tracker was tested. These results, together with those coming from the CMS global run, will provide the basis for the full-scale alignment of the Tracker, which will be carried out with the first \\emph{p-p} collisions.

  16. Needle custom search recall-oriented search on the web using semantic annotations

    NARCIS (Netherlands)

    Kaptein, R.; Koot, G.; Huis in 't Veld, M.A.A.; Broek, E.L. van den

    2014-01-01

    Web search engines are optimized for early precision, which makes it difficult to perform recall-oriented tasks using these search engines. In this article, we present our tool Needle Custom Search. This tool exploits semantic annotations of Web search results and, thereby, increase the efficiency o

  17. Needle custom search: recall-oriented search on the Web using semantic annotations

    NARCIS (Netherlands)

    Kaptein, Rianne; Koot, Gijs; Huis in 't Veld, Mirjam A.A.; Broek, van den Egon L.; Rijke, de Maarten; Kenter, Tom; Vries, de Arjen P.; Zhai, Chen Xiang; Jong, de Franciska; Radinsky, Kira; Hofmann, Katja

    2014-01-01

    Web search engines are optimized for early precision, which makes it difficult to perform recall-oriented tasks using these search engines. In this article, we present our tool Needle Custom Search. This tool exploits semantic annotations of Web search results and, thereby, increase the efficiency o

  18. Needle Custom Search : Recall-oriented search on the web using semantic annotations

    NARCIS (Netherlands)

    Kaptein, Rianne; Koot, Gijs; Huis in 't Veld, Mirjam A.A.; van den Broek, Egon L.

    2014-01-01

    Web search engines are optimized for early precision, which makes it difficult to perform recall-oriented tasks using these search engines. In this article, we present our tool Needle Custom Search. This tool exploits semantic annotations of Web search results and, thereby, increase the efficiency o

  19. Evaluation of microRNA alignment techniques.

    Science.gov (United States)

    Ziemann, Mark; Kaspi, Antony; El-Osta, Assam

    2016-08-01

    Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing. PMID:27284164

  20. Testing the tidal alignment model of galaxy intrinsic alignment

    International Nuclear Information System (INIS)

    Weak gravitational lensing has become a powerful probe of large-scale structure and cosmological parameters. Precision weak lensing measurements require an understanding of the intrinsic alignment of galaxy ellipticities, which can in turn inform models of galaxy formation. It is hypothesized that elliptical galaxies align with the background tidal field and that this alignment mechanism dominates the correlation between ellipticities on cosmological scales (in the absence of lensing). We use recent large-scale structure measurements from the Sloan Digital Sky Survey to test this picture with several statistics: (1) the correlation between ellipticity and galaxy overdensity, wg+; (2) the intrinsic alignment auto-correlation functions; (3) the correlation functions of curl-free, E, and divergence-free, B, modes, the latter of which is zero in the linear tidal alignment theory; (4) the alignment correlation function, wg(rp,θ), a recently developed statistic that generalizes the galaxy correlation function to account for the angle between the galaxy separation vector and the principle axis of ellipticity. We show that recent measurements are largely consistent with the tidal alignment model and discuss dependence on galaxy luminosity. In addition, we show that at linear order the tidal alignment model predicts that the angular dependence of wg(rp,θ) is simply wg+(rp)cos (2θ) and that this dependence is consistent with recent measurements. We also study how stochastic nonlinear contributions to galaxy ellipticity impact these statistics. We find that a significant fraction of the observed LRG ellipticity can be explained by alignment with the tidal field on scales ∼> 10 \\hMpc. These considerations are relevant to galaxy formation and evolution

  1. Accelerated Profile HMM Searches.

    Directory of Open Access Journals (Sweden)

    Sean R Eddy

    2011-10-01

    Full Text Available Profile hidden Markov models (profile HMMs and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the "multiple segment Viterbi" (MSV algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call "sparse rescaling". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches.

  2. Fast multi-blind modification search through tandem mass spectrometry.

    Science.gov (United States)

    Na, Seungjin; Bandeira, Nuno; Paek, Eunok

    2012-04-01

    With great biological interest in post-translational modifications (PTMs), various approaches have been introduced to identify PTMs using MS/MS. Recent developments for PTM identification have focused on an unrestrictive approach that searches MS/MS spectra for all known and possibly even unknown types of PTMs at once. However, the resulting expanded search space requires much longer search time and also increases the number of false positives (incorrect identifications) and false negatives (missed true identifications), thus creating a bottleneck in high throughput analysis. Here we introduce MODa, a novel "multi-blind" spectral alignment algorithm that allows for fast unrestrictive PTM searches with no limitation on the number of modifications per peptide while featuring over an order of magnitude speedup in relation to existing approaches. We demonstrate the sensitivity of MODa on human shotgun proteomics data where it reveals multiple mutations, a wide range of modifications (including glycosylation), and evidence for several putative novel modifications. Based on the reported findings, we argue that the efficiency and sensitivity of MODa make it the first unrestrictive search tool with the potential to fully replace conventional restrictive identification of proteomics mass spectrometry data. PMID:22186716

  3. Google Power Search

    CERN Document Server

    Spencer, Stephan

    2011-01-01

    Behind Google's deceptively simple interface is immense power for both market and competitive research-if you know how to use it well. Sure, basic searches are easy, but complex searches require specialized skills. This concise book takes you through the full range of Google's powerful search-refinement features, so you can quickly find the specific information you need. Learn techniques ranging from simple Boolean logic to URL parameters and other advanced tools, and see how they're applied to real-world market research examples. Incorporate advanced search operators such as filetype:, intit

  4. Search for vector-like T' quarks using tools for the analysis of jet substructure with the CMS experiment

    International Nuclear Information System (INIS)

    A search for pairs of vector-like T' quark produced in proton-proton collisions recorded with the CMS experiment at √(s)=8 TeV is presented. The search is optimized for decays of T' quarks to top quarks and Higgs bosons, where the top quarks and Higgs bosons decay hadronically. The T'-quark mass range between 500 and 1000 GeV is investigated. The top quarks and Higgs bosons produced in decays of the heavy T' quarks acquire large Lorentz boosts. The signatures of these particles in the detector can overlap and are therefore difficult to resolve using classical jet reconstruction methods. Large-radius jets are reconstructed and subjets formed from their constituents. The decay products of particles with large Lorentz boosts are highly collimated and can all be found within a single one of these large-radius jets. Top jets containing hadronic top-quark decays are identified with a top-tagging algorithm that analyzes the jet substructure. A b-tagging algorithm is applied to the reconstructed subjets in order to find bottom quarks within the jet substructure. In order to identify Higgs bosons with large Lorentz boosts decaying to pairs of bottom quarks, the Higgs-tagging algorithm searches for two b-tagged subjets within a single jet. This is the first application of a top-tagging algorithm in conjunction with subjet b-tagging in an analysis of CMS data. Also, a Higgs-tagging algorithm is used for the first time in a search for new physics. The main background contributions to this analysis consist of pair-produced top quarks and QCD-multijet events. More than 99% of these events are rejected by the event selection based on the new jet-substructure methods, while 6-8% of the signal events are retained. A description for the QCD-multijet background is obtained from data in a method also using jet-substructure information. Bayesian exclusion limits are derived from a likelihood ratio in which two discriminating variables are combined. T' quarks

  5. Aligning for Innovation - Alignment Strategy to Drive Innovation

    Science.gov (United States)

    Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

    2010-01-01

    With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

  6. Vertically aligned patterned peptide nanowires for cellulars studies

    DEFF Research Database (Denmark)

    Taskin, Mehmet; Sasso, Luigi; Vedarethinam, Indumathi;

    2012-01-01

    . Recently, our group has demonstrated that vertically aligned diphenylalanine based peptide nanowires (VAPNW) are an useful tool for cellular studies and sensor applications. To expand this study, we patterned VAPNWs into strips of various widths onto an electrode surface to evaluate these structures...... as laminine. Combining this work with other approaches like discrete functionalization of VAPNWs will reveal possible future tools for cellular studies and biosensing....

  7. Application for surveying technology for the alignment of large optical systems

    International Nuclear Information System (INIS)

    Precise alignment of optical elements in large optical systems is difficult if many elements are positioned such that direct alignment or boresighting becomes impossible. A practical approach is to identify discrete optical path segments and align these using standard surveying or optical-tooling instrumentation. One simply has to develop an alignment theory in which the alignment optical path duplicates or closely approximates the optical path of the operational device. The surveying instruments can then be used to simulate the optical input beams to the system segments to be aligned. Auxiliary targets and reflectors may be added, and the alignment procedure may be augmented by standard optical test instrumentation and techniques. Examples are given using theodolites, transits, and levels with autocollimating capability and micrometer adaptors to perform boresighting and autocollimation techniques on segments of the optical train of the Antares Laser Fusion System at Los Alamos National Laboratory

  8. Muon System alignment with tracks

    CERN Document Server

    Calderón, Alicia; Virto, A L; Martínez, P; Martínez-Rivero, C; Matorras, Francisco; Rodrigo, Teresa; Sobron, M; Vila, Ivan

    2006-01-01

    We describe here some of the techniques foreseen to align the Muon System with muon tracks. Two methods are proposed, one based on the Tracker which measures the position of a Muon chamber with respect to the Tracker, and another one which aligns internally the Muon System. A mathematical model is described for the general case. It is simplified for several particular cases of the Muon System alignment and applied to realistic examples on full simulation. Some estimates of the expected precision and limitation of the method are presented.

  9. ALIGNMENT BETWEEN A BUSINESS STRATEGY AND THE CUSTOMER RELACIONSHIP MANAGEMENT: CASE OF A PHONE COMPANY

    OpenAIRE

    Evandro Prieto; Fernando José Barbin Laurindo; Marly Monteiro de Carvalho

    2007-01-01

    The aim of this paper is to discuss the strategic alignment between business and customers’ need as a critical factor in the definition and creation of sustainable competitive advantage. By this point of view, the CRM (Customer Relationship Management) is considered as a strategic tool to make possible this alignment. The methodology selected to conduct this work was the case study in a phone company. The objective is to investigate the evolution and the stage of the alignment....

  10. In Search of Practitioner-Based Social Capital: A Social Network Analysis Tool for Understanding and Facilitating Teacher Collaboration in a US-Based STEM Professional Development Program

    Science.gov (United States)

    Baker-Doyle, Kira J.; Yoon, Susan A.

    2011-01-01

    This paper presents the first in a series of studies on the informal advice networks of a community of teachers in an in-service professional development program. The aim of the research was to use Social Network Analysis as a methodological tool to reveal the social networks developed by the teachers, and to examine whether these networks…

  11. Tracking and Alignment in the CMS detector

    CERN Document Server

    Ronga, Frederic Jean

    2007-01-01

    This Report summarises the alignment strategy of the CMS detector. Track reconstruction in the silicon tracker and muon chambers is briefly described. We then present the different sources of alignment information, in particular alignment algorithms using reconstructed tracks.

  12. A new automatic alignment technology for single mode fiber-waveguide based on improved genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yu; CHEN Zhuang-zhuang; LI Ya-juan; DUAN Jian

    2009-01-01

    A novel automatic alignment algorithm of single mode fiber-waveguide based on improved genetic algorithm is proposed. The genetic searching is based on the dynamic crossover operator and the adaptive mutation operator to solve the premature convergence of simple genetic algorithm The improved genetic algorithm combines with hill-climbing method and pattern searching algorithm, to solve low precision of simple genetic algorithm in later searching. The simulation results indicate that the improved genetic algorithm can rise the alignment precision and reach the coupling loss of 0.01 dB when platform moves near 207 space points averagely.

  13. Harmonic Analysis of Linac Alignment

    CERN Document Server

    McCrady, Rodney C

    2005-01-01

    We have analyzed the requirements on alignment of the focusing elements (quadrupole doublets) in the Los Alamos Neutron Science Center (LANSCE) side coupled linac. The analysis is performed in terms of harmonics of the quardrupole spacing. This allows us to determine the effect of intentional deviations from a straight line, such as following the curvature of the Earth, and of unintentional deviations introduced by measurement and alignment errors. Results are compared to measured positions of the doublets.

  14. Expressive alignment language and implementation

    OpenAIRE

    Euzenat, Jérôme; Scharffe, François; Zimmermann, Antoine

    2007-01-01

    euzenat2007e This deliverable provides the description of an alignment language which is both expressive and independent from ontology languages. It defines the language through its abstract syntax and semantics depending on ontology language semantics. It then describes two concrete syntax: an exchange syntax in RDF/XML and a surface syntax for human consumption. Finally, it presents the current implementation of this expressive language within the Alignment API taking advantage of the OM...

  15. Heuristic reusable dynamic programming: efficient updates of local sequence alignment.

    Science.gov (United States)

    Hong, Changjin; Tewfik, Ahmed H

    2009-01-01

    Recomputation of the previously evaluated similarity results between biological sequences becomes inevitable when researchers realize errors in their sequenced data or when the researchers have to compare nearly similar sequences, e.g., in a family of proteins. We present an efficient scheme for updating local sequence alignments with an affine gap model. In principle, using the previous matching result between two amino acid sequences, we perform a forward-backward alignment to generate heuristic searching bands which are bounded by a set of suboptimal paths. Given a correctly updated sequence, we initially predict a new score of the alignment path for each contour to select the best candidates among them. Then, we run the Smith-Waterman algorithm in this confined space. Furthermore, our heuristic alignment for an updated sequence shows that it can be further accelerated by using reusable dynamic programming (rDP), our prior work. In this study, we successfully validate "relative node tolerance bound" (RNTB) in the pruned searching space. Furthermore, we improve the computational performance by quantifying the successful RNTB tolerance probability and switch to rDP on perturbation-resilient columns only. In our searching space derived by a threshold value of 90 percent of the optimal alignment score, we find that 98.3 percent of contours contain correctly updated paths. We also find that our method consumes only 25.36 percent of the runtime cost of sparse dynamic programming (sDP) method, and to only 2.55 percent of that of a normal dynamic programming with the Smith-Waterman algorithm. PMID:19875856

  16. Long Read Alignment with Parallel MapReduce Cloud Platform.

    Science.gov (United States)

    Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

    2015-01-01

    Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms. PMID:26839887

  17. Concept Search

    OpenAIRE

    Giunchiglia, Fausto; Kharkevich, Uladzimir; Zaihrayeu, Ilya

    2008-01-01

    In this paper we present a novel approach, called Concept Search, which extends syntactic search, i.e., search based on the computation of string similarity between words, with semantic search, i.e., search based on the computation of semantic relations between concepts. The key idea of Concept Search is to operate on complex concepts and to maximally exploit the semantic information available, reducing to syntactic search only when necessary, i.e., when no semantic information is available. ...

  18. Precision crystal alignment for high-resolution electron microscope imaging

    International Nuclear Information System (INIS)

    One of the more difficult tasks involved in obtaining quality high-resolution electron micrographs is the precise alignment of a specimen into the required zone. The current accepted procedure, which involves changing to diffraction mode and searching for symmetric point diffraction pattern, is insensitive to small amounts of misalignment and at best qualitative. On-line analysis of the fourier space representation of the image, both for determining and correcting crystal tilt, is investigated. 8 refs., 42 figs

  19. Evaluation of Federated Searching Options for the School Library

    Science.gov (United States)

    Abercrombie, Sarah E.

    2008-01-01

    Three hosted federated search tools, Follett One Search, Gale PowerSearch Plus, and WebFeat Express, were configured and implemented in a school library. Databases from five vendors and the OPAC were systematically searched. Federated search results were compared with each other and to the results of the same searches in the database's native…

  20. 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

  1. A real-time all-atom structural search engine for proteins.

    Directory of Open Access Journals (Sweden)

    Gabriel Gonzalez

    2014-07-01

    Full Text Available Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license, https://github.com/Gabriel439/suns-cmd (command line client, BSD license, and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license.

  2. Alignment without Magnet Fiducials

    Energy Technology Data Exchange (ETDEWEB)

    Ruland, Robert; /SLAC; Mulhaupt, Gottfried; Rohrer, Martin; Wiegand, Peter; /PSI, Villigen

    2005-08-17

    Presently, the demand for high quality synchrotron radiation is increasing all over the world. One of the fascinating aspects of this novel tool is the broad range of scientific users interested in synchrotron radiation. They come from physics, chemistry, biology, and medicine, to name just a few. Third generation storage which recently became available for users will by far not be able to satisfy all the beam-time requests. In addition, it is also recognized that long-term scientific efficiency and technological success is heavily dependent on ease of access to a home based facility nearby and continuing fine-tuning of all components of a beam line. Based on the high quality user community in Switzerland and their prospective research activities, the Paul Scherrer Institute, in close collaboration with interested research groups from the Swiss universities and the Swiss Federal Institutes of Technology, has worked out a proposal to build an advanced synchrotron light source in Switzerland, which will come into operation in the year 2001. It has been named SLS as acronym for Swiss Light Source.

  3. High-throughput sequence alignment using Graphics Processing Units

    Directory of Open Access Journals (Sweden)

    Trapnell Cole

    2007-12-01

    Full Text Available Abstract Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.

  4. How to build a DNA search engine like Google?

    OpenAIRE

    Liang, Wang; Bo, Fang

    2010-01-01

    This paper proposed a new method to build the large scale DNA sequences search system based on web search engine technology. We give a very brief introduction for the methods used in search engine first. Then how to build a DNA search system like Google is illustrated in detail. Since there is no local alignment process, this system is able to provide the ms level search services for billions of DNA sequences in a typical server.

  5. Professional Microsoft search fast search, Sharepoint search, and search server

    CERN Document Server

    Bennett, Mark; Kehoe, Miles; Voskresenskaya, Natalya

    2010-01-01

    Use Microsoft's latest search-based technology-FAST search-to plan, customize, and deploy your search solutionFAST is Microsoft's latest intelligent search-based technology that boasts robustness and an ability to integrate business intelligence with Search. This in-depth guide provides you with advanced coverage on FAST search and shows you how to use it to plan, customize, and deploy your search solution, with an emphasis on SharePoint 2010 and Internet-based search solutions.With a particular appeal for anyone responsible for implementing and managing enterprise search, this book presents t

  6. Alignment and calibration of a focal neurotransmitter uncaging system.

    Science.gov (United States)

    Sarkisov, Dmitry V; Wang, Samuel S-H

    2006-01-01

    Photolysis of caged compounds is a powerful tool for studying subcellular physiological functions. Here we describe protocols for the alignment and calibration of a focal uncaging system. We also report procedures for convenient quantitative calibration of uncaging. Using these methods, we can achieve submicron lateral resolution of photolysis and probe biological function in spines, the smallest signaling compartments of neurons. Initially, the entire alignment procedure takes 4-6 h to perform; periodic fine-tuning of the system takes 1-2 h. PMID:17406314

  7. Aligned electrospun polymer fibres for skeletal muscle regeneration

    Directory of Open Access Journals (Sweden)

    KJ Aviss

    2010-05-01

    Full Text Available Skeletal muscle repair is often overlooked in surgical procedures and in serious burn victims. Creating a tissue-engineered skeletal muscle would not only provide a grafting material for these clinical situations, but could also be used as a valuable true-to-life research tool into diseases affecting muscle tissue. Electrospinning of the elastomer PLGA produced aligned fibres that had the correct topology to provide contact guidance for myoblast elongation and alignment. In addition, the electrospun scaffold required no surface modifications or incorporation of biologic material for adhesion, elongation, and differentiation of C2C12 murine myoblasts.

  8. Field-free long-lived alignment of molecules in extreme rotational states

    CERN Document Server

    Milner, A A; Milner, V

    2015-01-01

    We introduce a new optical tool - a "two-dimensional optical centrifuge", capable of aligning molecules in extreme rotational states. Unlike the conventional centrifuge, which confines the molecules in the plane of their rotation, its two-dimensional version aligns the molecules along a well-defined axis, similarly to the effect of a single linearly polarized laser pulse, but at a much higher level of rotational excitation. The increased robustness of ultra-high rotational states with respect to collisions results in a longer life time of the created alignment in dense media, offering new possibilities for studying and utilizing aligned molecular ensembles under ambient conditions.

  9. Application of integer programming on logistics solution for load transportation: the solver tool and its limitations in the search for the optimal solution

    Directory of Open Access Journals (Sweden)

    Ricardo França Santos

    2012-01-01

    Full Text Available This work tries to solve a typical logistics problem of Navy of Brazil regards the allocation, transportation and distribution of genera refrigerated for Military Organizations within Grande Rio (RJ. After a brief review of literature on Linear/Integer Programming and some of their applications, we proposed the use of Integer Programming, using the Excel’s Solver as a tool for obtaining the optimal load configuration for the fleet, obtaining the lower distribution costs in order to meet the demand schedule. The assumptions were met in a first attempt with a single spreadsheet, but it could not find a convergent solution, without degeneration problems and with a reasonable solution time. A second solution was proposed separating the problem into three phases, which allowed us to highlight the potential and limitations of the Solver tool. This study showed the importance of formulating a realistic model and of a detailed critical analysis, which could be seen through the lack of convergence of the first solution and the success achieved by the second one.

  10. Tools For Installing Keys On A Stud

    Science.gov (United States)

    Goodoak, Robert D.

    1995-01-01

    Two tools designed to be used together to drive long locking keys axially to install them on stud. Tools are: supporter holding keys in correct relative alignment and driver having multiple prongs, each of which fits into one of holes in supporter. Tools prevent bending and breaking of keys during installation, and make possible to install all keys simultaneously, in one motion.

  11. Geodetic alignment of laser power installations

    International Nuclear Information System (INIS)

    Main problems occuring in applied geodesy under initial alignment of laser power installation optical channel are considered. Attention is paid to alignment of lens beamguide telescopic pairs and alignment quality control. Methods and means of geodetic measurements under alignment are indicated. Conclusions are made about the degree of working through certain aspects of the problem

  12. Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome.

    Science.gov (United States)

    Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

    2010-01-01

    MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs. PMID:21364831

  13. Interactive Video Search

    OpenAIRE

    Schoeffmann, Klaus; Hopfgartner, Frank

    2015-01-01

    With an increasing amount of video data in our daily life, the need for content-based search in videos increases as well. Though a lot of research has been spent on video retrieval tools and methods which allow for automatic search in videos through content-based queries, still the performance of automatic video retrieval is far from optimal. In this tutorial we discussed (i) proposed solutions for improved video content navigation, (ii) typical interaction of content-based querying features,...

  14. Better searching through science.

    Science.gov (United States)

    Voss, D

    2001-09-14

    The explosive growth of the World Wide Web has produced frustration for researchers seeking quality content and pinpoint results among the noise and spam. Now, a handful of companies and academic researchers are working on a new breed of search engines to undo this second curse of Babel. These next-generation search tools will let scientists drill deeper into the billion-page Web. PMID:11557874

  15. Search Cloud

    Science.gov (United States)

    ... https://www.nlm.nih.gov/medlineplus/cloud.html Search Cloud To use the sharing features on this page, please enable JavaScript. Share the MedlinePlus search cloud with your users by embedding our search ...

  16. Search Tips

    Science.gov (United States)

    ... do not need to use AND because the search engine automatically finds resources containing all of your search ... Use as a wildcard when you want the search engine to fill in the blank for you; you ...

  17. Search Cloud

    Science.gov (United States)

    ... this page: https://medlineplus.gov/cloud.html Search Cloud To use the sharing features on this page, ... Top 110 zoster vaccine Share the MedlinePlus search cloud with your users by embedding our search cloud ...

  18. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  19. Strategic Alignment and New Product Development

    DEFF Research Database (Denmark)

    Acur, Nuran; Kandemir, Destan; Boer, Harry

    2012-01-01

    Strategic alignment is widely accepted as a prerequisite for a firm’s success, but insight into the role of alignment in, and its impact on, the new product evelopment (NPD) process and its performance is less well developed. Most publications on this topic either focus on one form of alignment or...... of NPD performance indicators. Strategic planning and innovativeness appear to affect technological, market, and NPD-marketing alignment positively. Environmental munificence is negatively associated with NPD-marketing alignment, but has no effect on the two other forms of alignment. Technological...... change has a positive effect on technological alignment, a negative effect on NPD-marketing alignment, but no effect on market alignment. These findings suggest that internal capabilities are more likely to be associated with the development of strategic alignment than environmental factors are...

  20. CRIRES-VLT high-resolution spectro-astrometry as a tool in the search of small structures at the cores of Planetary Nebulae

    CERN Document Server

    Cárdenas, Mónica W Blanco; Guerrero, Martín A; Miranda, Luis F; Seifahrt, Andreas

    2014-01-01

    The onset of the asymmetry in planetary nebulae (PNe) occurs during the short transition between the end of the asymptotic giant branch (AGB) phase and the beginning of the PN phase. Sources in this transition phase are compact and emit intensely in infrared wavelengths, making high spatial resolution observations in the infrared mandatory to investigate the shaping process of PNe. Interferometric VLTI IR observations have revealed compelling evidence of disks at the cores of PNe, but the limited sensitivity, strong observational constraints, and limited spatial coverage place severe limits on the universal use of this technique. Inspired by the successful detection of proto-planetary disks using spectro-astrometric observations, we apply here for the first time this technique to search for sub-arcsecond structures in PNe. Our exploratory study using CRIRES (CRyogenic high-resolution Infra-Red Echelle Spectrograph) commissioning data of the proto-PN IRAS 17516-2525 and the young PN SwSt 1 has revealed small-s...

  1. Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

    Directory of Open Access Journals (Sweden)

    Skolnick Jeffrey

    2008-12-01

    Full Text Available Abstract Background Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed alignment, which is extended and/or refined to provide the best structural superposition between a pair of protein structures as assessed by a structure comparison metric. One such metric, the TM-score, was recently introduced to provide a combined structure quality measure of the coordinate root mean square deviation between a pair of structures and coverage. Using the TM-score, the TM-align structure alignment algorithm was developed that was often found to have better accuracy and coverage than the most commonly used structural alignment programs; however, there were a number of situations when this was not true. Results To further improve structure alignment quality, the Fr-TM-align algorithm has been developed where aligned fragment pairs are used to generate the initial seed alignments that are then refined using dynamic programming to maximize the TM-score. For the assessment of the structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TM-align, we examined various alignment quality assessment scores such as PSI and TM-score. The assessment showed that the structural alignment quality from Fr-TM-align is better in comparison to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have a higher TM-score (~9% and coverage (~7% in comparison to those generated by TM-align. Fr-TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is computationally more expensive than TM-align. Conclusion Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The source code and executables of Fr-TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/.

  2. Topology independent protein structural alignment

    Directory of Open Access Journals (Sweden)

    DasGupta Bhaskar

    2007-10-01

    Full Text Available Abstract Background Identifying structurally similar proteins with different chain topologies can aid studies in homology modeling, protein folding, protein design, and protein evolution. These include circular permuted protein structures, and the more general cases of non-cyclic permutations between similar structures, which are related by non-topological rearrangement beyond circular permutation. We present a method based on an approximation algorithm that finds sequence-order independent structural alignments that are close to optimal. We formulate the structural alignment problem as a special case of the maximum-weight independent set problem, and solve this computationally intensive problem approximately by iteratively solving relaxations of a corresponding integer programming problem. The resulting structural alignment is sequence order independent. Our method is also insensitive to insertions, deletions, and gaps. Results Using a novel similarity score and a statistical model for significance p-value, we are able to discover previously unknown circular permuted proteins between nucleoplasmin-core protein and auxin binding protein, between aspartate rasemase and 3-dehydrogenate dehydralase, as well as between migration inhibition factor and arginine repressor which involves an additional strand-swapping. We also report the finding of non-cyclic permuted protein structures existing in nature between AML1/core binding factor and ribofalvin synthase. Our method can be used for large scale alignment of protein structures regardless of the topology. Conclusion The approximation algorithm introduced in this work can find good solutions for the problem of protein structure alignment. Furthermore, this algorithm can detect topological differences between two spatially similar protein structures. The alignment between MIF and the arginine repressor demonstrates our algorithm's ability to detect structural similarities even when spatial

  3. A business intelligence approach using web search tools and online data reduction techniques to examine the value of product-enabled services

    DEFF Research Database (Denmark)

    Tanev, Stoyan; Liotta, Giacomo; Kleismantas, Andrius

    2015-01-01

    in Canada and Europe. It adopts an innovative methodology based on online textual data that could be implemented in advanced business intelligence tools aiming at the facilitation of innovation, marketing and business decision making. Combinations of keywords referring to different aspects of service value...... is based on the fact that existing studies on the value attributes of hybrid offerings are mostly conceptual and need to be further substantiated through more systematic empirical studies. The research includes two samples with a total of 83 product-driven firms selected among the top R&D spenders......, and customer satisfaction. The service value attributes for the European firms include, among others, product added-value, product modernization and optimization of customer time and efforts. Canadian firms focus on collaboration and co-creation with suppliers and customers for the sake of product...

  4. Aligned Layers of Silver Nano-Fibers

    OpenAIRE

    Golovin, Andrii B.; Liubov Kreminska; Jeremy Stromer

    2012-01-01

    We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polariz...

  5. Measurements of magnetic field alignment

    International Nuclear Information System (INIS)

    The procedure for installing Superconducting Super Collider (SSC) dipoles in their respective cryostats involves aligning the average direction of their field with the vertical to an accuracy of 0.5 mrad. The equipment developed for carrying on these measurements is described and the measurements performed on the first few prototypes SSC magnets are presented. The field angle as a function of position in these 16.6 m long magnets is a characteristic of the individual magnet with possible feedback information to its manufacturing procedure. A comparison of this vertical alignment characteristic with a magnetic field intensity (by NMR) characteristic for one of the prototypes is also presented. 5 refs., 7 figs

  6. XUV ionization of aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

    Kelkensberg, F.; Siu, W.; Gademann, G. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Rouzee, A.; Vrakking, M. J. J. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Max-Born-Institut, Max-Born Strasse 2A, D-12489 Berlin (Germany); Johnsson, P. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Department of Physics, Lund University, Post Office Box 118, SE-221 00 Lund (Sweden); Lucchini, M. [Department of Physics, Politecnico di Milano, Istituto di Fotonica e Nanotecnologie CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  7. Position list word aligned hybrid

    DEFF Research Database (Denmark)

    Deliege, Francois; Pedersen, Torben Bach

    2010-01-01

    Compressed bitmap indexes are increasingly used for efficiently querying very large and complex databases. The Word Aligned Hybrid (WAH) bitmap compression scheme is commonly recognized as the most efficient compression scheme in terms of CPU efficiency. However, WAH compressed bitmaps use a lot...... of storage space. This paper presents the Position List Word Aligned Hybrid (PLWAH) compression scheme that improves significantly over WAH compression by better utilizing the available bits and new CPU instructions. For typical bit distributions, PLWAH compressed bitmaps are often half the size of WAH...

  8. Volume visualization of multiple alignment of genomic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Nameeta; Weber, Gunther H.; Dillard, Scott E.; Hamann, Bernd

    2004-05-01

    Genomes of hundreds of species have been sequenced to date and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive ''billion basepair DNA sequences'' becomes substantial, so does the need for more powerful tools supporting the exploration of these data sets. Similarity score data used to compare aligned DNA sequences is inherently one-dimensional. One-dimensional (1D) representations of these data sets do not effectively utilize screen real estate. We present a technique to arrange 1D data in 3D space to allow us to apply state-of-the-art interactive volume visualization techniques for data exploration. We provide results for aligned DNA sequence data and compare it with traditional 1D line plots. Our technique, coupled with 1D line plots, results in effective multiresolution visualization of very large aligned sequence data sets.

  9. Alignment-Free Methods for the Detection and Specificity Prediction of Adenylation Domains.

    Science.gov (United States)

    Agüero-Chapin, Guillermin; Pérez-Machado, Gisselle; Sánchez-Rodríguez, Aminael; Santos, Miguel Machado; Antunes, Agostinho

    2016-01-01

    Identifying adenylation domains (A-domains) and their substrate specificity can aid the detection of nonribosomal peptide synthetases (NRPS) at genome/proteome level and allow inferring the structure of oligopeptides with relevant biological activities. However, that is challenging task due to the high sequence diversity of A-domains (~10-40 % of amino acid identity) and their selectivity for 50 different natural/unnatural amino acids. Altogether these characteristics make their detection and the prediction of their substrate specificity a real challenge when using traditional sequence alignment methods, e.g., BLAST searches. In this chapter we describe two workflows based on alignment-free methods intended for the identification and substrate specificity prediction of A-domains. To identify A-domains we introduce a graphical-numerical method, implemented in TI2BioP version 2.0 (topological indices to biopolymers), which in a first step uses protein four-color maps to represent A-domains. In a second step, simple topological indices (TIs), called spectral moments, are derived from the graphical representations of known A-domains (positive dataset) and of unrelated but well-characterized sequences (negative set). Spectral moments are then used as input predictors for statistical classification techniques to build alignment-free models. Finally, the resulting alignment-free models can be used to explore entire proteomes for unannotated A-domains. In addition, this graphical-numerical methodology works as a sequence-search method that can be ensemble with homology-based tools to deeply explore the A-domain signature and cope with the diversity of this class (Aguero-Chapin et al., PLoS One 8(7):e65926, 2013). The second workflow for the prediction of A-domain's substrate specificity is based on alignment-free models constructed by transductive support vector machines (TSVMs) that incorporate information of uncharacterized A-domains. The construction of the models was

  10. TPX: Biomedical literature search made easy

    OpenAIRE

    Joseph, Thomas; Saipradeep, Vangala G; Raghavan, Ganesh Sekar Venkat; Srinivasan, Rajgopal; Rao, Aditya; Kotte, Sujatha; Sivadasan, Naveen

    2012-01-01

    TPX is a web-based PubMed search enhancement tool that enables faster article searching using analysis and exploration features. These features include identification of relevant biomedical concepts from search results with linkouts to source databases, concept based article categorization, concept assisted search and filtering, query refinement. A distinguishing feature here is the ability to add user-defined concept names and/or concept types for named entity recognition. The tool allows co...

  11. First-order aggregation models with alignment

    Science.gov (United States)

    Fetecau, Razvan C.; Sun, Weiran; Tan, Changhui

    2016-06-01

    We include alignment interactions in a well-studied first-order attractive-repulsive macroscopic model for aggregation. The distinctive feature of the extended model is that the equation that specifies the velocity in terms of the population density, becomes implicit, and can have non-unique solutions. We investigate the well-posedness of the model and show rigorously how it can be obtained as a macroscopic limit of a second-order kinetic equation. We work within the space of probability measures with compact support and use mass transportation ideas and the characteristic method as essential tools in the analysis. A discretization procedure that parallels the analysis is formulated and implemented numerically in one and two dimensions.

  12. Nanofiber alignment of a small diameter elastic electrospun scaffold

    Science.gov (United States)

    Patel, Jignesh

    Cardiovascular disease is the leading cause of death in western countries with coronary heart disease making up 50% of these deaths. As a treatment option, tissue engineered grafts have great potential. Elastic scaffolds that mimic arterial extracellular matrix (ECM) may hold the key to creating viable vascular grafts. Electrospinning is a widely used scaffold fabrication technique to engineer tubular scaffolds. In this study, we investigated how the collector rotation speed altered the nanofiber alignment which may improve mechanical characteristics making the scaffold more suitable for arterial grafts. The scaffold was fabricated from a blend of PCL/Elastin. 2D Fast Fourier Transform (FFT) image processing tool and MatLab were used to quantitatively analyze nanofiber orientation at different collector speeds (13500 to 15500 rpm). Both Image J and MatLab showed graphical peaks indicating predominant fiber orientation angles. A collector speed of 15000 rpm was found to produce the best nanofiber alignment with narrow peaks at 90 and 270 degrees, and a relative amplitude of 200. This indicates a narrow distribution of circumferentially aligned nanofibers. Collector speeds below and above 15000 rpm caused a decrease in fiber alignment with a broader orientation distribution. Uniformity of fiber diameter was also measured. Of 600 measures from the 15000 rpm scaffolds, the fiber diameter range from 500 nm to 899 nm was most prevalent. This diameter range was slightly larger than native ECM which ranges from 50 nm to 500 nm. The second most prevalent diameter range had an average of 404 nm which is within the diameter range of collagen. This study concluded that with proper electrospinning technique and collector speed, it is possible to fabricate highly aligned small diameter elastic scaffolds. Image J 2D FFT results confirmed MatLab findings for the analyses of circumferentially aligned nanofibers. In addition, MatLab analyses simplified the FFT orientation data

  13. Embedding strategies for effective use of information from multiple sequence alignments.

    OpenAIRE

    Henikoff, S; Henikoff, J G

    1997-01-01

    We describe a new strategy for utilizing multiple sequence alignment information to detect distant relationships in searches of sequence databases. A single sequence representing a protein family is enriched by replacing conserved regions with position-specific scoring matrices (PSSMs) or consensus residues derived from multiple alignments of family members. In comprehensive tests of these and other family representations, PSSM-embedded queries produced the best results overall when used with...

  14. 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...

  15. Aligned natural inflation with modulations

    Science.gov (United States)

    Choi, Kiwoon; Kim, Hyungjin

    2016-08-01

    The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  16. Aligned natural inflation with modulations

    CERN Document Server

    Choi, Kiwoon

    2015-01-01

    The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  17. Aligned natural inflation with modulations

    Directory of Open Access Journals (Sweden)

    Kiwoon Choi

    2016-08-01

    Full Text Available The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  18. Aligned natural inflation with modulations

    OpenAIRE

    Kiwoon Choi; Hyungjin Kim

    2016-01-01

    The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  19. Looking for New Naturally Aligned Higgs Doublets at the LHC

    CERN Document Server

    Dev, P S Bhupal

    2015-01-01

    Since the current LHC Higgs data suggest the couplings of the observed 125 GeV Higgs boson to be close to the Standard Model (SM) expectations, any extended Higgs sector must lead to the so-called SM alignment limit, where one of the Higgs bosons behaves exactly like that of the SM. In the context of the Two Higgs Doublet Model (2HDM), this alignment is often associated with either decoupling of the heavy Higgs sector or accidental cancellations in the 2HDM potential. We present a novel symmetry justification for 'natural' alignment without necessarily decoupling or fine-tuning. We show that there exist only three different symmetry realizations of the natural alignment scenario in 2HDM. We analyze new collider signals for the heavy Higgs sector in the natural alignment limit, which dominantly lead to third-generation quarks in the final state and can serve as a useful observational tool during the Run-II phase of the LHC.

  20. Long Read Alignment with Parallel MapReduce Cloud Platform

    Directory of Open Access Journals (Sweden)

    Ahmed Abdulhakim Al-Absi

    2015-01-01

    Full Text Available Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner’s Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms.

  1. Search Engine Optimization For Dummies

    CERN Document Server

    Kent, Peter

    2012-01-01

    Increase your online ranking with this beginner guide to SEO! Search engine optimization (SEO) is an integral part of getting a site to rank high in the various search engines in order to attract potential customers. With this new edition of a bestseller, you?ll learn the ins and outs and best practices of successful SEO in order to make your website content more search-engine friendly so that it ranks higher among search engines and draws high-volume traffic. Covers search engine basics to help you get started Introduces new coverage on content marketing and reuse, new tracking tools, platfor

  2. iTRAQ and multiple reaction monitoring as proteomic tools for biomarker search in cerebrospinal fluid of patients with Parkinson's disease dementia.

    Science.gov (United States)

    Lehnert, Stefan; Jesse, Sarah; Rist, Wolfgang; Steinacker, Petra; Soininen, Hilkka; Herukka, Sanna-Kaisa; Tumani, Hayrettin; Lenter, Martin; Oeckl, Patrick; Ferger, Boris; Hengerer, Bastian; Otto, Markus

    2012-04-01

    About 30% of patients with Parkinson's disease (PD) develop Parkinson's disease dementia (PDD) in the course of the disease. Until now, diagnosis is based on clinical and neuropsychological examinations, since so far there is no laboratory marker. In this study we aimed to find a neurochemical marker which would allow a risk assessment for the development of a dementia in PD patients. For this purpose, we adopted a gel-free proteomic approach (iTRAQ-method) to identify biomarker-candidates in the cerebrospinal fluid (CSF) of patients with PD, PDD and non-demented controls (NDC). Validation of these candidates was then carried out by multiple-reaction-monitoring (MRM) optimised for CSF. Using the iTRAQ-approach, we were able to identify 16 differentially regulated proteins. Fourteen out of these 16 proteins could then be followed-up simultaneously in our optimised MRM-measurement protocol. However only Tyrosine-kinase-non-receptor-type 13 and Netrin-G1 differed significantly between PDD and NDC cohorts. In addition, a significant difference was found for Golgin-160 and Apolipoprotein B-100 between PD and NDC. Apart from possible pathophysiological considerations, we propose that Tyrosine-kinase non-receptor-type 13 and Netrin G1 are biomarker candidates for the development of a Parkinson's disease dementia. Furthermore we suggest that iTRAQ and MRM are valuable tools for the discovery of biomarker in cerebrospinal fluid. However further validation studies need to be done with larger patient cohorts and other proteins need to be checked as well. PMID:22327139

  3. Search Patterns

    CERN Document Server

    Morville, Peter

    2010-01-01

    What people are saying about Search Patterns "Search Patterns is a delight to read -- very thoughtful and thought provoking. It's the most comprehensive survey of designing effective search experiences I've seen." --Irene Au, Director of User Experience, Google "I love this book! Thanks to Peter and Jeffery, I now know that search (yes, boring old yucky who cares search) is one of the coolest ways around of looking at the world." --Dan Roam, author, The Back of the Napkin (Portfolio Hardcover) "Search Patterns is a playful guide to the practical concerns of search interface design. It cont

  4. Spectral library searching in proteomics.

    Science.gov (United States)

    Griss, Johannes

    2016-03-01

    Spectral library searching has become a mature method to identify tandem mass spectra in proteomics data analysis. This review provides a comprehensive overview of available spectral library search engines and highlights their distinct features. Additionally, resources providing spectral libraries are summarized and tools presented that extend experimental spectral libraries by simulating spectra. Finally, spectrum clustering algorithms are discussed that utilize the same spectrum-to-spectrum matching algorithms as spectral library search engines and allow novel methods to analyse proteomics data. PMID:26616598

  5. Clean Cities Tools

    Energy Technology Data Exchange (ETDEWEB)

    None

    2014-12-19

    The U.S. Department of Energy's Clean Cities offers a large collection of Web-based tools on the Alternative Fuels Data Center. These calculators, interactive maps, and data searches can assist fleets, fuels providers, and other transportation decision makers in their efforts to reduce petroleum use.

  6. Detecting the limits of regulatory element conservation anddivergence estimation using pairwise and multiple alignments

    Energy Technology Data Exchange (ETDEWEB)

    Pollard, Daniel A.; Moses, Alan M.; Iyer, Venky N.; Eisen,Michael B.

    2006-08-14

    Background: Molecular evolutionary studies of noncodingsequences rely on multiple alignments. Yet how multiple alignmentaccuracy varies across sequence types, tree topologies, divergences andtools, and further how this variation impacts specific inferences,remains unclear. Results: Here we develop a molecular evolutionsimulation platform, CisEvolver, with models of background noncoding andtranscription factor binding site evolution, and use simulated alignmentsto systematically examine multiple alignment accuracy and its impact ontwo key molecular evolutionary inferences: transcription factor bindingsite conservation and divergence estimation. We find that the accuracy ofmultiple alignments is determined almost exclusively by the pairwisedivergence distance of the two most diverged species and that additionalspecies have a negligible influence on alignment accuracy. Conservedtranscription factor binding sites align better than surroundingnoncoding DNA yet are often found to be misaligned at relatively shortdivergence distances, such that studies of binding site gain and losscould easily be confounded by alignment error. Divergence estimates frommultiple alignments tend to be overestimated at short divergencedistances but reach a tool specific divergence at which they cease toincrease, leading to underestimation at long divergences. Our moststriking finding was that overall alignment accuracy, binding sitealignment accuracy and divergence estimation accuracy vary greatly acrossbranches in a tree and are most accurate for terminal branches connectingsister taxa and least accurate for internal branches connectingsub-alignments. Conclusions: Our results suggest that variation inalignment accuracy can lead to errors in molecular evolutionaryinferences that could be construed as biological variation. Thesefindings have implications for which species to choose for analyses, whatkind of errors would be expected for a given set of species and howmultiple alignment tools and

  7. Prism Window for Optical Alignment

    Science.gov (United States)

    Tang, Hong

    2008-01-01

    A prism window has been devised for use, with an autocollimator, in aligning optical components that are (1) required to be oriented parallel to each other and/or at a specified angle of incidence with respect to a common optical path and (2) mounted at different positions along the common optical path. The prism window can also be used to align a single optical component at a specified angle of incidence. Prism windows could be generally useful for orienting optical components in manufacture of optical instruments. "Prism window" denotes an application-specific unit comprising two beam-splitter windows that are bonded together at an angle chosen to obtain the specified angle of incidence.

  8. Aligning seminars with Bologna requirements

    DEFF Research Database (Denmark)

    Lueg, Klarissa; Lueg, Rainer; Lauridsen, Ole

    2015-01-01

    Changes in public policy, such as the Bologna Process, require students to be equipped with multifunctional competencies to master relevant tasks in unfamiliar situations. Achieving this goal might imply a change in many curricula toward deeper learning. As a didactical means to achieve deep...... learning results, the authors suggest reciprocal peer tutoring (RPT); as a conceptual framework the authors suggest the SOLO (Structure of Observed Learning Outcomes) taxonomy and constructive alignment as suggested by Biggs and Tang. Our study presents results from the introduction of RPT in a large...... course. The authors find that RPT produces satisfying learning outcomes, active students, and ideal constructive alignments of the seminar content with the exam, the intended learning outcomes, and the requirements of the Bologna Process. Our data, which comprise surveys and evaluations from both faculty...

  9. Aligned mesoporous architectures and devices.

    Energy Technology Data Exchange (ETDEWEB)

    Brinker, C. Jeffrey; Lu, Yunfeng (University of California Los Angeles, Los Angeles, CA)

    2011-03-01

    This is the final report for the Presidential Early Career Award for Science and Engineering - PECASE (LDRD projects 93369 and 118841) awarded to Professor Yunfeng Lu (Tulane University and University of California-Los Angeles). During the last decade, mesoporous materials with tunable periodic pores have been synthesized using surfactant liquid crystalline as templates, opening a new avenue for a wide spectrum of applications. However, the applications are somewhat limited by the unfavorabe pore orientation of these materials. Although substantial effort has been devoted to align the pore channels, fabrication of mesoporous materials with perpendicular pore channels remains challenging. This project focused on fabrication of mesoporous materials with perpendicularly aligned pore channels. We demonstrated structures for use in water purification, separation, sensors, templated synthesis, microelectronics, optics, controlled release, and highly selective catalysts.

  10. RDF Graph Alignment with Bisimulation

    OpenAIRE

    Buneman, Peter; Staworko, Sławek

    2016-01-01

    We investigate the problem of aligning two RDF databases, an essential problem in understanding the evolution of ontologies. Our approaches address three fundamental challenges: 1) the use of "blank" (null) names, 2) ontology changes in which different names are used to identify the same entity, and 3) small changes in the data values as well as small changes in the graph structure of the RDF database. We propose approaches inspired by the classical notion of graph bisimulation and extend the...

  11. Interest alignment and competitive advantage

    OpenAIRE

    Gottschalg, Oliver; Zollo, Mauricio

    2006-01-01

    This paper articulates a theory of the conditions under which the alignment between individual and collective interests generates sustainable competitive advantage. The theory is based on the influence of tacitness, context-specificity and casual ambiguity in the determinants of different types of motivation (extrinsic, normative intrinsic and hedonic intrinsic), under varying conditions of environmental dynamism. The analysis indicates the need to consider mitivational processes as a complem...

  12. SIM Lite: ground alignment of the instrument

    Science.gov (United States)

    Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

    2010-07-01

    We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

  13. Intrinsic Galaxy Alignments and Weak Gravitational Lensing

    CERN Document Server

    Heavens, A F

    2001-01-01

    Gravitational lensing causes background galaxy images to become aligned, and the statistical characteristics of the image alignments can then be used to constrain the power spectrum of mass fluctuations. Analyses of gravitational lensing assume that intrinsic galaxy alignments are negligible, but if this assumption does not hold, then the interpretation of image alignments will be in error. As gravitational lensing experiments become more ambitious and seek very low-level alignments arising from lensing by large-scale structure, it becomes more important to estimate the level of intrinsic alignment in the galaxy population. In this article, I review the cluster of independent theoretical studies of this issue, as well as the current observational status. Theoretically, the calculation of intrinsic alignments is by no means straightforward, but some consensus has emerged from the existing works, despite each making very different assumptions. This consensus is that a) intrinsic alignments are a small but non-n...

  14. Incorporating evolution of transcription factor binding sites into annotated alignments

    Indian Academy of Sciences (India)

    Abha S Bais; Steffen Grossmann; Martin Vingron

    2007-08-01

    Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms. A common strategy is to combine cross-species conservation with single sequence TFBS annotation to yield ``conserved TFBSs”. Most current methods in this field adopt a multi-step approach that segregates the two aspects. Again, it is widely accepted that the evolutionary dynamics of binding sites differ from those of the surrounding sequence. Hence, it is desirable to have an approach that explicitly takes this factor into account. Although a plethora of approaches have been proposed for the prediction of conserved TFBSs, very few explicitly model TFBS evolutionary properties, while additionally being multi-step. Recently, we introduced a novel approach to simultaneously align and annotate conserved TFBSs in a pair of sequences. Building upon the standard Smith-Waterman algorithm for local alignments, SimAnn introduces additional states for profiles to output extended alignments or annotated alignments. That is, alignments with parts annotated as gaplessly aligned TFBSs (pair-profile hits) are generated. Moreover, the pair-profile related parameters are derived in a sound statistical framework. In this article, we extend this approach to explicitly incorporate evolution of binding sites in the SimAnn framework. We demonstrate the extension in the theoretical derivations through two position-specific evolutionary models, previously used for modelling TFBS evolution. In a simulated setting, we provide a proof of concept that the approach works given the underlying assumptions, as compared to the original work. Finally, using a real dataset of experimentally verified binding sites in human-mouse sequence pairs, we compare the new approach (eSimAnn) to an existing multi-step tool that also considers TFBS evolution. Although it is widely accepted that binding sites evolve differently from the surrounding sequences, most comparative TFBS identification

  15. Visualization of multiple alignments, phylogenies and gene family evolution.

    Science.gov (United States)

    Procter, James B; Thompson, Julie; Letunic, Ivica; Creevey, Chris; Jossinet, Fabrice; Barton, Geoffrey J

    2010-03-01

    Software for visualizing sequence alignments and trees are essential tools for life scientists. In this review, we describe the major features and capabilities of a selection of stand-alone and web-based applications useful when investigating the function and evolution of a gene family. These range from simple viewers, to systems that provide sophisticated editing and analysis functions. We conclude with a discussion of the challenges that these tools now face due to the flood of next generation sequence data and the increasingly complex network of bioinformatics information sources. PMID:20195253

  16. Alignment in star-debris disc systems seen by Herschel

    CERN Document Server

    Greaves, J S; Thureau, N; Eiroa, C; Marshall, J P; Maldonado, J; Matthews, B C; Olofsson, G; Barlow, M J; Moro-Martin, A; Sibthorpe, B; Absil, O; Ardila, D R; Booth, M; Broekhoven-Fiene, H; Brown, D J A; Cameron, A Collier; del Burgo, C; Di Francesco, J; Duchene, G; Eisloffel, J; Ertel, S; Holland, W S; Horner, J; Kalas, P; Kavelaars, J J; Lestrade, J -F; Vican, L; Wilner, D J; Wolf, S; Wyatt, M C

    2013-01-01

    Many nearby main-sequence stars have been searched for debris using the far-infrared Herschel satellite, within the DEBRIS, DUNES and Guaranteed-Time Key Projects. We discuss here 11 stars of spectral types A to M where the stellar inclination is known and can be compared to that of the spatially-resolved dust belts. The discs are found to be well aligned with the stellar equators, as in the case of the Sun's Kuiper belt, and unlike many close-in planets seen in transit surveys. The ensemble of stars here can be fitted with a star-disc tilt of ~<10 degrees. These results suggest that proposed mechanisms for tilting the star or disc in fact operate rarely. A few systems also host imaged planets, whose orbits at tens of AU are aligned with the debris discs, contrary to what might be expected in models where external perturbers induce tilts.

  17. Suspended photonic waveguide arrays for submicrometer alignment

    OpenAIRE

    Peters, T. J.; Tichem, M.; Staufer, U.

    2014-01-01

    This paper presents a new alignment concept for the alignment of multichannel photonic intergrated circuits (PICs) using flexible photonic waveguides on one of the PICs that are positionable by integrated micro electro mechanical system (MEMS) actuators. The concept aims for high precision and high degree of assembly process automation. The proposed concept includes pre-alignment of both PICs on a common substrate followed by fine-alignment using the on-chip flexible waveguides and MEMS funct...

  18. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    OpenAIRE

    Hasan, L.

    2011-01-01

    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of protein or DNA sequences. An accurate alignment can provide valuable information for experimentation on the newly found sequences. It is indispensable in basic research as well as in practical applic...

  19. Trust and Transparency from an Alignment Perspective

    OpenAIRE

    Gryning, Morten

    2015-01-01

    The academic literature suggests that firms cannot stay competitive if their business and IT departments are not aligned. Several theories have provided insights into how to achieve alignment, yet most IT and business departments still struggle to fulfill each other’s expectations, with dissatisfaction and low trust as a result. Some scholars argue that alignment is about finding the right mechanical configuration for a given organization. Others argue that alignment theory should...

  20. Inferring comprehensible business/ICT alignment rules.

    OpenAIRE

    Cumps, Bjorn; Martens, David; De Backer, Manu; Haesen, Raf; Viaene, Stijn; Dedene, Guido; Baesens, Bart; Snoeck, Monique

    2009-01-01

    We inferred business rules for business/ICT alignment by applying a novel rule induction algorithm on a data set containing rich alignment information polled from 641 organisations in 7 European countries. The alignment rule set was created using AntMiner+, a rule induction technique with a reputation of inducing accurate, comprehensible, and intuitive predictive models from data. Our data set consisted of 18 alignment practices distilled from an analysis of relevant publications and validate...

  1. MIMOX: a web tool for phage display based epitope mapping

    Directory of Open Access Journals (Sweden)

    Honda Wataru

    2006-10-01

    Full Text Available Abstract Background Phage display is widely used in basic research such as the exploration of protein-protein interaction sites and networks, and applied research such as the development of new drugs, vaccines, and diagnostics. It has also become a promising method for epitope mapping. Research on new algorithms that assist and automate phage display based epitope mapping has attracted many groups. Most of the existing tools have not been implemented as an online service until now however, making it less convenient for the community to access, utilize, and evaluate them. Results We present MIMOX, a free web tool that helps to map the native epitope of an antibody based on one or more user supplied mimotopes and the antigen structure. MIMOX was coded in Perl using modules from the Bioperl project. It has two sections. In the first section, MIMOX provides a simple interface for ClustalW to align a set of mimotopes. It also provides a simple statistical method to derive the consensus sequence and embeds JalView as a Java applet to view and manage the alignment. In the second section, MIMOX can map a single mimotope or a consensus sequence of a set of mimotopes, on to the corresponding antigen structure and search for all of the clusters of residues that could represent the native epitope. NACCESS is used to evaluate the surface accessibility of the candidate clusters; and Jmol is embedded to view them interactively in their 3D context. Initial case studies show that MIMOX can reproduce mappings from existing tools such as FINDMAP and 3DEX, as well as providing novel, rational results. Conclusion A web-based tool called MIMOX has been developed for phage display based epitope mapping. As a publicly available online service in this area, it is convenient for the community to access, utilize, and evaluate, complementing other existing programs. MIMOX is freely available at http://web.kuicr.kyoto-u.ac.jp/~hjian/mimox.

  2. PepeSearch: Semantic Data for the Masses

    OpenAIRE

    Guillermo Vega-Gorgojo; Martin Giese; Simen Heggestøyl; Ahmet Soylu; Arild Waaler

    2016-01-01

    With the emergence of the Web of Data, there is a need of tools for searching and exploring the growing amount of semantic data. Unfortunately, such tools are scarce and typically require knowledge of SPARQL/RDF. We propose here PepeSearch, a portable tool for searching semantic datasets devised for mainstream users. PepeSearch offers a multi-class search form automatically constructed from a SPARQL endpoint. We have tested PepeSearch with 15 participants searching a Linked Open Data version ...

  3. A Feedback-Based Web Search Engine

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei-feng; XU Bao-wen; ZHOU Xiao-yu

    2004-01-01

    Web search engines are very useful information service tools in the Internet.The current web search engines produce search results relating to the search terms and the actual information collected by them.Since the selections of the search results cannot affect the future ones, they may not cover most people's interests.In this paper, feedback information produced by the users' accessing lists will be represented by the rough set and can reconstruct the query string and influence the search results.And thus the search engines can provide self-adaptability.

  4. Beam alignment system for laser welding system

    International Nuclear Information System (INIS)

    The patent describes a beam alignment system for laser welding work pieces, such as fuel rod grids for nuclear fuel assemblies. The apparatus for performing various laser-machining comprises a beam alignment system including alignment target means, as well as means for emitting, directing and focusing the laser beam. (U.K.)

  5. Physician-Hospital Alignment in Orthopedic Surgery.

    Science.gov (United States)

    Bushnell, Brandon D

    2015-09-01

    The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. PMID:26375539

  6. Vertically aligned nanostructure scanning probe microscope tips

    Science.gov (United States)

    Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.

    2006-12-19

    Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

  7. Ultrafast electron diffraction from aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

    Centurion, Martin [Univ. of Nebraska, Lincoln, NE (United States)

    2015-08-17

    The aim of this project was to record time-resolved electron diffraction patterns of aligned molecules and to reconstruct the 3D molecular structure. The molecules are aligned non-adiabatically using a femtosecond laser pulse. A femtosecond electron pulse then records a diffraction pattern while the molecules are aligned. The diffraction patterns are then be processed to obtain the molecular structure.

  8. Technology Outlook as a tool for the management of innovation

    Directory of Open Access Journals (Sweden)

    Jon Mikel Zabala-Iturriagagoitia

    2012-03-01

    Full Text Available The purpose of this paper is to present a theoretical overview of innovation management and the tools that can aid in this endeavour. The paper adopts a user-oriented description, aiming at making SMEs familiar with the possibilities opened by innovation management tools in general and technology outlook in particular.The goal of technology outlook is to search, interpret and evaluate information on technological developments in the areas of interest for the company. The process is divided into three general stages: observe, analyze and use. The paper explores all dimensions included in these stages together with the requirements for their implementation in the context of SMEs. In addition we also introduce the roles required for such a process to systematically work: observers, analysts and decision makers. These roles correspond to the previous three stages, so observers are involved during the first step, analysts are related to the second phase and decision makers to the final exploitation.The paper closes by raising some concerns as to why innovation management tools in general and technology outlook in particular are underused in the context of SMEs. The author concludes that if SMEs are to increase their innovative potential, this challenge will be to a great extent dependent on their ability to introduce innovation management routines and tools aligned with their general strategies.

  9. Nsite, NsiteH and NsiteM Computer Tools for Studying Tran-scription Regulatory Elements

    KAUST Repository

    Shahmuradov, Ilham A.

    2015-07-02

    Summary: Gene transcription is mostly conducted through interactions of various transcription factors and their binding sites on DNA (regulatory elements, REs). Today, we are still far from understanding the real regulatory content of promoter regions. Computer methods for identification of REs remain a widely used tool for studying and understanding transcriptional regulation mechanisms. The Nsite, NsiteH and NsiteM programs perform searches for statistically significant (non-random) motifs of known human, animal and plant one-box and composite REs in a single genomic sequence, in a pair of aligned homologous sequences and in a set of functionally related sequences, respectively.

  10. Personalized Search

    CERN Document Server

    AUTHOR|(SzGeCERN)749939

    2015-01-01

    As the volume of electronically available information grows, relevant items become harder to find. This work presents an approach to personalizing search results in scientific publication databases. This work focuses on re-ranking search results from existing search engines like Solr or ElasticSearch. This work also includes the development of Obelix, a new recommendation system used to re-rank search results. The project was proposed and performed at CERN, using the scientific publications available on the CERN Document Server (CDS). This work experiments with re-ranking using offline and online evaluation of users and documents in CDS. The experiments conclude that the personalized search result outperform both latest first and word similarity in terms of click position in the search result for global search in CDS.

  11. Integrated Alignment and Inspection Platform for High Precision Optical Continuous Images

    OpenAIRE

    Chuen-Horng Lin; Muh-Don Hsiao; Chun-Chi Lo

    2014-01-01

    This platform is mainly intended to be used as a facility for high precision optical continuous images. Then, with a fixed pattern being selected, this platform can quickly search, with resistance to variation, the mark that corresponds to the pattern in order to achieve the alignment and inspection target. Since the pattern is a minute component with multiple shapes and unstable features, this platform can automatically acquire it through the system or select it by user. The targets searched...

  12. Analytical Searching.

    Science.gov (United States)

    Pappas, Marjorie L.

    1995-01-01

    Discusses analytical searching, a process that enables searchers of electronic resources to develop a planned strategy by combining words or phrases with Boolean operators. Defines simple and complex searching, and describes search strategies developed with Boolean logic and truncation. Provides guidelines for teaching students analytical…

  13. Aligning molecules with intense nonresonant laser fields

    DEFF Research Database (Denmark)

    Larsen, J.J.; Safvan, C.P.; Sakai, H.;

    1999-01-01

    Molecules in a seeded supersonic beam are aligned by the interaction between an intense nonresonant linearly polarized laser field and the molecular polarizability. We demonstrate the general applicability of the scheme by aligning I2, ICl, CS2, CH3I, and C6H5I molecules. The alignment is probed by...... mass selective two dimensional imaging of the photofragment ions produced by femtosecond laser pulses. Calculations on the degree of alignment of I2 are in good agreement with the experiments. We discuss some future applications of laser aligned molecules....

  14. Providing Curriculum Support in the School Library Media Center: Resource Alignment, or How To Eat an Elephant.

    Science.gov (United States)

    Lowe, Karen

    2003-01-01

    Discusses the process of weeding, updating, and building a school library media collection that supports the state curriculum. Explains resource alignment, a process for using the shelf list as a tool to analyze and align media center resources to state curricula, and describes a five-year plan and its usefulness for additional funding. (LRW)

  15. How accurately is ncRNA aligned within whole-genome multiple alignments?

    Directory of Open Access Journals (Sweden)

    Ruzzo Walter L

    2007-10-01

    Full Text Available Abstract Background Multiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated. Results We evaluate the alignment accuracy of certain noncoding regions using noncoding RNA alignments from Rfam as a reference. We inspect the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for all the human sequences in the Rfam seed alignments. In particular, we find 638 instances of chimeric and partial alignments to human noncoding RNA elements, of which at least 225 can be improved by straightforward means. As a byproduct of our procedure, we predict many novel instances of known ncRNA families that are suggested by the alignment. Conclusion MULTIZ does a fairly accurate job of aligning these genomes in these difficult regions. However, our experiments indicate that better alignments exist in some regions.

  16. Multiscale peak alignment for chromatographic datasets.

    Science.gov (United States)

    Zhang, Zhi-Min; Liang, Yi-Zeng; Lu, Hong-Mei; Tan, Bin-Bin; Xu, Xiao-Na; Ferro, Miguel

    2012-02-01

    Chromatography has been extensively applied in many fields, such as metabolomics and quality control of herbal medicines. Preprocessing, especially peak alignment, is a time-consuming task prior to the extraction of useful information from the datasets by chemometrics and statistics. To accurately and rapidly align shift peaks among one-dimensional chromatograms, multiscale peak alignment (MSPA) is presented in this research. Peaks of each chromatogram were detected based on continuous wavelet transform (CWT) and aligned against a reference chromatogram from large to small scale gradually, and the aligning procedure is accelerated by fast Fourier transform cross correlation. The presented method was compared with two widely used alignment methods on chromatographic dataset, which demonstrates that MSPA can preserve the shapes of peaks and has an excellent speed during alignment. Furthermore, MSPA method is robust and not sensitive to noise and baseline. MSPA was implemented and is available at http://code.google.com/p/mspa. PMID:22222564

  17. Antares beam-alignment-system performance

    International Nuclear Information System (INIS)

    The beam alignment system for the 24-beam-sector Antares CO2 fusion laser automatically aligns more than 200 optical elements. A visible-wavelength alignment technique is employed which uses a telescope/TV system to view point-light sources appropriately located down the beamline. The centroids of the light spots are determined by a video tracker, which generates error signals used by the computer control system to move appropriate mirrors in a closed-loop system. Final touch-up alignment is accomplished by projecting a CO2 alignment laser beam through the system and sensing its position at the target location. The techniques and control algorithms employed have resulted in alignment accuracies exceeding design requirements. By employing video processing to determine the centroids of diffraction images and by averaging over multiple TV frames, we achieve alignment accuracies better than 0.1 times system diffraction limits in the presence of air turbulence

  18. Pupil Alignment Measuring Technique and Alignment Reference for Instruments or Optical Systems

    Science.gov (United States)

    Hagopian, John G.

    2010-01-01

    A technique was created to measure the pupil alignment of instruments in situ by measuring calibrated pupil alignment references (PARs) in instruments. The PAR can also be measured using an alignment telescope or an imaging system. PAR allows the verification of the science instrument (SI) pupil alignment at the integrated science instrument module (ISIM) level of assembly at ambient and cryogenic operating temperature. This will allow verification of the ISIM+SI alignment, and provide feedback to realign the SI if necessary.

  19. How accurately is ncRNA aligned within whole-genome multiple alignments?

    OpenAIRE

    Ruzzo Walter L; Wang Adrienne X; Tompa Martin

    2007-01-01

    Abstract Background Multiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated. Results We evaluate the alignment accuracy of certain noncoding regions using noncoding RNA alignments from Rfam as a reference. We inspect the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for...

  20. Search Engines for Tomorrow's Scholars, Part Two

    Science.gov (United States)

    Fagan, Jody Condit

    2012-01-01

    This two-part article considers how well some of today's search tools support scholars' work. The first part of the article reviewed Google Scholar and Microsoft Academic Search using a modified version of Carole L. Palmer, Lauren C. Teffeau, and Carrier M. Pirmann's framework (2009). Microsoft Academic Search is a strong contender when…

  1. Alignment of the SLC Final Focus system using beam orbits

    International Nuclear Information System (INIS)

    Beam based alignment is being routinely applied in the SLC Final Focus and has proved to be a very useful tool for determining the quality of the zeroth order orbit as defined by various beam line elements. Given the stringent requirement on the beam quality at the interaction point, a well aligned beam line is essential in that it minimizes the confusion which would otherwise arise in the higher order optics, the demand called on the correctors which also serve as optical knobs, and the problem associated with the background radiation. In the SLC final focus we have been relying on an interplay between the field survey and the orbit analysis to achieve this purpose. Mechanical alignment generally provides coordinate information of various beam line elements and offset values inferred from these data and the model of the beam line. Beam based alignment is done mainly by recording the beam orbit under controlled experiment where optical elements or orbit conditions are varied. Due to the complexity of the beamline layout and special power supply configuration in the SLC Final Focus, the latter method is useful only when coupled with off-line analysis which disentangles the data taken at each measurement. In this report we describe the techniques used and the underlying principle, the procedure as applied in the Final Focus, the outcome of this exercise and some problems encountered. 6 figs

  2. High-harmonic generation in aligned water molecules

    Science.gov (United States)

    Wang, Song; Devin, Julien; Hoffmann, Matthias; Cryan, James; Kaldun, Andreas; Bucksbaum, Philip

    2016-05-01

    In recent years, the use of high harmonic generation (HHG) in aligned molecular vapors has become a powerful tool to study ultrafast dynamics of electronic and nuclear wave packets. In our new experimental setup, we are able to orient H2 O and D2 O molecules using a single cycle terahertz (THz) pulse. Aligning water is especially interesting as the highest occupied molecular orbital (HOMO) of water contains a node in the xz plane of the molecular frame, allowing us to perform HHG from second highest occupied molecular orbital (HOMO-1) only, by setting the polarization of the fundamental laser along the z-axis of the aligned water molecules. We are particularly interested in the HOMO-1 state, as there is fast motion of the H-O-H angle leading to sub-wavelength dynamics. On this poster we present our all-optical alignment setup where HHG and single-cycle THz generation take place in high-vacuum, where measurements with arbitrary polarization angles between the two are possible. In addition, we discuss the effects of the molecular orientation on HHG, including symmetry breaking that could produce even harmonics and isotope effects between H2 O and D2 O due to different vibrational energies. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

  3. Laser Safety: A Laser Alignment Practical Training Course

    Energy Technology Data Exchange (ETDEWEB)

    Woods, Michael; Edstrom, Steve; /SLAC

    2011-01-26

    SLAC National Accelerator Laboratory has developed a Laser Alignment Practical Training Course as one of its core laser safety classes. The course is taught to small groups of up to three students and takes 1-3 hours to complete. This practical course is not a substitute for site-specific On-the-Job Training; it does, however, provide a good introduction in core laser safety practices that can be broadly applied. Alignment and diagnostic tasks are performed with low power lasers. Students learn safe alignment and diagnostic techniques and how to avoid common mistakes that might lead to an accident. The class is taught by laser supervisors, enabling them to assess the skill level of new laser personnel and determine the subsequent level of supervision needed. The course has six alignment tasks. For each task, discussion points are given for the instructor to review with the students. The optics setup includes different wavelength lasers, a beam expander, mirrors, irises, a periscope, a beam-splitting polarizer and a diffraction grating. Diagnostic tools include viewing cards, an IR viewer and a ccd camera. Laser eyewear is available to block some laser wavelengths in the setup.

  4. NON-ALIGNEMENT IN AFRICA

    Directory of Open Access Journals (Sweden)

    G. Jacobs

    2012-02-01

    Full Text Available The first indications to the Western world that African non-alignment had achieved conscious political form became apparent only in the late 1940's. This strand of thought within the tapestry of Africanism reached its zenith with the declarations of Kwame Nkrumah, Jomo Kenyatta and Julius Nyerere in the years after the Pan-African Congress in Manchester in 1945. The causes of the movement go back far beyond the first official expressions of an African solidarity in the 1940's. As a mature expression of group attitudes tqwards foreign pol icy, nonalignment can be traced back to the roots of African nationalism.

  5. The Cluster Substructure - Alignment Connection

    CERN Document Server

    Plionis, M

    2002-01-01

    Using the APM cluster data we investigate whether the dynamical status of clusters is related to the large-scale structure of the Universe. We find that cluster substructure is strongly correlated with the tendency of clusters to be aligned with their nearest neighbour and in general with the nearby clusters that belong to the same supercluster. Furthermore, dynamically young clusters are more clustered than the overall cluster population. These are strong indications that cluster develop in a hierarchical fashion by anisotropy merging along the large-scale filamentary superclusters within which they are embedded.

  6. The Substructure-Alignment Connection

    CERN Document Server

    Plionis, M; Plionis, Manolis; Basilakos, Spyros

    2001-01-01

    Using a sample of 903 APM clusters we investigate whether their dynamical status, as evidenced by the presence of significant substructures, is related to the large-scale structure of the Universe. We find that the cluster dynamical activity is strongly correlated with the tendency of clusters to be aligned with their nearest neighbour and in general with the nearby clusters that belong to the same supercluster. Furthermore, dynamically active clusters are more clustered than the overall cluster population. These are strong indications that clusters develop in a hierarchical fashion by anisotropic merging along the large-scale filaments within which they are embedded.

  7. Aligned interactions in cosmic rays

    Science.gov (United States)

    Kempa, J.

    2015-12-01

    The first clean Centauro was found in cosmic rays years many ago at Mt Chacaltaya experiment. Since that time, many people have tried to find this type of interaction, both in cosmic rays and at accelerators. But no one has found a clean cases of this type of interaction.It happened finally in the last exposure of emulsion at Mt Chacaltaya where the second clean Centauro has been found. The experimental data for both the Centauros and STRANA will be presented and discussed in this paper. We also present our comments to the intriguing question of the existence of a type of nuclear interactions at high energy with alignment.

  8. Aligned interactions in cosmic rays

    Energy Technology Data Exchange (ETDEWEB)

    Kempa, J., E-mail: kempa@pw.plock.pl [Warsaw University of Technology Branch Plock (Poland)

    2015-12-15

    The first clean Centauro was found in cosmic rays years many ago at Mt Chacaltaya experiment. Since that time, many people have tried to find this type of interaction, both in cosmic rays and at accelerators. But no one has found a clean cases of this type of interaction.It happened finally in the last exposure of emulsion at Mt Chacaltaya where the second clean Centauro has been found. The experimental data for both the Centauros and STRANA will be presented and discussed in this paper. We also present our comments to the intriguing question of the existence of a type of nuclear interactions at high energy with alignment.

  9. Strategies for active alignment of lenses

    Science.gov (United States)

    Langehanenberg, Patrik; Heinisch, Josef; Wilde, Chrisitan; Hahne, Felix; Lüerß, Bernd

    2015-10-01

    Today's optical systems require up-to-date assembly and joining technology. The trend of keeping dimensions as small as possible while maintaining or increasing optical imaging performance leaves little to no room for mechanical lens adjustment equipment that may remain in the final product. In this context active alignment of optical elements opens up possibilities for the fast and cost-economic manufacturing of lenses and lens assemblies with highest optical performance. Active alignment for lens manufacturing is the precise alignment of the optical axis of a lens with respect to an optical or mechanical reference axis (e.g. housing) including subsequent fixation by glue. In this contribution we will describe different approaches for active alignment and outline strengths and limitations of the different methods. Using the SmartAlign principle, highest quality cemented lenses can be manufactured without the need for high precision prealignment, while the reduction to a single alignment step greatly reduces the cycle time. The same strategies can also be applied to bonding processes. Lenses and lens groups can be aligned to both mechanical and optical axes to maximize the optical performance of a given assembly. In hybrid assemblies using both mechanical tolerances and active alignment, SmartAlign can be used to align critical lens elements anywhere inside the system for optimized total performance. Since all geometrical parameters are re-measured before each alignment, this process is especially suited for complex and time-consuming production processes where the stability of the reference axis would otherwise be critical. For highest performance, lenses can be actively aligned using up to five degrees of freedom. In this way, SmartAlign enables the production of ultra-precise mounted lenses with an alignment precision below 1 μm.

  10. Alignment of ICNP® 2.0 Ontology and a proposed INCP® Brazilian Ontology

    OpenAIRE

    Carina Maris Gaspar Carvalho; Marcia Regina Cubas; Andreia Malucelli; Maria Miriam Lima da Nóbrega

    2014-01-01

    OBJECTIVE: to align the International Classification for Nursing Practice (ICNP®) Version 2.0 ontology and a proposed INCP® Brazilian Ontology.METHOD: document-based, exploratory and descriptive study, the empirical basis of which was provided by the ICNP® 2.0 Ontology and the INCP® Brazilian Ontology. The ontology alignment was performed using a computer tool with algorithms to identify correspondences between concepts, which were organized and analyzed according to their presence or absence...

  11. Alignment of service characteristics with competitive strategy & customer satisfaction : A Comparative study in fast food industry

    OpenAIRE

    Goraya, Muneeb; Zaaroura, Ibrahim

    2016-01-01

    Competitive strategies are an essential tool for sustainable competitive advantage. Particularly in the service industry, strategy has its significance as it plays a vital role in achieving customer satisfaction. This study investigates alignment of four service characteristics i.e. servicescape, service quality, quality and value with the firms’ strategy and how this alignment achieves customer satisfaction. A set of hypotheses were formulated to portray the significance of each of the four ...

  12. Multiple whole genome alignments and novel biomedical applications at the VISTA portal

    OpenAIRE

    Brudno, Michael; Poliakov, Alexander; Minovitsky, Simon; Ratnere, Igor; Dubchak, Inna

    2007-01-01

    The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the visualization of the results. The VISTA portal also hosts alignments of a number of genomes computed by our group, allowing users to study regions of their interest without having to manually download the individual sequences. Here we describe various algorithmic and functional improvements implement...

  13. Gene functional similarity search tool (GFSST)

    OpenAIRE

    Russo James J; Sheng Huitao; Zhang Jinghui; Zhang Peisen; Osborne Brian; Buetow Kenneth

    2006-01-01

    Abstract Background With the completion of the genome sequences of human, mouse, and other species and the advent of high throughput functional genomic research technologies such as biomicroarray chips, more and more genes and their products have been discovered and their functions have begun to be understood. Increasing amounts of data about genes, gene products and their functions have been stored in databases. To facilitate selection of candidate genes for gene-disease research, genetic as...

  14. Toxics Release Inventory Pollution Prevention Search Tool

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Toxics Release Inventory (TRI) is a publicly available EPA database that contains information on toxic chemical releases and waste management and pollution...

  15. A Toolbox of Metrology-Based Techniques for Optical System Alignment

    Science.gov (United States)

    Coulter, Phillip; Ohl, Raymond G.; Blake, Peter N.; Bos, Brent J.; Casto, Gordon V.; Eichhorn, William L.; Gum, Jeffrey S.; Hadjimichael, Theodore J.; Hagopian, John G.; Hayden, Joseph E.; Hicks, Samantha L.; Kubalak, Dave; Mclean, Kyle F.; McMann, Joseph; Redman, Kevin; Wenzel, Greg; Young, Jerrod

    2016-01-01

    The NASA Goddard Space Flight Center (GSFC) and its partners have broad experience in the alignment of flight optical instruments and spacecraft structures. Over decades, GSFC developed alignment capabilities and techniques for a variety of optical and aerospace applications. In this paper, we provide an overview of a subset of the capabilities and techniques used on several recent projects in a toolbox format. We discuss a range of applications, from small-scale optical alignment of sensors to mirror and bench examples that make use of various large-volume metrology techniques. We also discuss instruments and analytical tools.

  16. Fossil evidence for spin alignment of Sloan Digital Sky Survey galaxies in filaments

    NARCIS (Netherlands)

    Jones, Bernard J. T.; van de Weijgaert, Marinus; Aragon-Calvo, Miguel A.

    2010-01-01

    We search for and find fossil evidence that the spin axes of galaxies in cosmic web filaments relative to their host filaments are not randomly distributed. This indicates the fact that the action of large-scale tidal torques affected the alignments of galaxies located in cosmic filaments. To this e

  17. Volume visualization of multiple alignment of large genomicDNA

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Nameeta; Dillard, Scott E.; Weber, Gunther H.; Hamann, Bernd

    2005-07-25

    Genomes of hundreds of species have been sequenced to date, and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive ''billion basepair DNA sequences'' becomes substantial, so does the need for more powerful tools supporting the exploration of these data sets. Similarity score data used to compare aligned DNA sequences is inherently one-dimensional. One-dimensional (1D) representations of these data sets do not effectively utilize screen real estate. As a result, tools using 1D representations are incapable of providing informatory overview for extremely large data sets. We present a technique to arrange 1D data in 3D space to allow us to apply state-of-the-art interactive volume visualization techniques for data exploration. We demonstrate our technique using multi-millions-basepair-long aligned DNA sequence data and compare it with traditional 1D line plots. The results show that our technique is superior in providing an overview of entire data sets. Our technique, coupled with 1D line plots, results in effective multi-resolution visualization of very large aligned sequence data sets.

  18. Visa undulator fiducialization and alignment

    International Nuclear Information System (INIS)

    As part of the R and D program towards a fourth generation light source, a Self-Amplified Spontaneous Emission (SASE) demonstration is being prepared. The Visible-Infrared SASE Amplifier (VISA) undulator will be installed at Brookhaven National Laboratory by the end of the year. The VISA undulator is an in-vacuum, 4-meter long, 1.8 cm period, pure-permanent magnet device, with a novel, strong focusing, permanent magnet FODO array included within the fixed, 6 mm undulator gap. The undulator is constructed of 99 cm long segments. To attain maximum SASE gain requires establishing overlap of electron and photon beams to within 50 μm rms. This imposes challenging tolerances on mechanical fabrication and magnetic field quality, and necessitates use of laser straightness interferometry for calibration and alignment of the magnetic axes of the undulator segments. This paper describes the magnetic centerline determination, and the fiducialization and alignment processes which were performed to meet the tolerance goal. (authors)

  19. Accelerated convergence and robust asymptotic regression of the Gumbel scale parameter for gapped sequence alignment

    International Nuclear Information System (INIS)

    Searches through biological databases provide the primary motivation for studying sequence alignment statistics. Other motivations include physical models of annealing processes or mathematical similarities to, e.g., first-passage percolation and interacting particle systems. Here, we investigate sequence alignment statistics, partly to explore two general mathematical methods. First, we model the global alignment of random sequences heuristically with Markov additive processes. In sequence alignment, the heuristic suggests a numerical acceleration scheme for simulating an important asymptotic parameter (the Gumbel scale parameter λ). The heuristic might apply to similar mathematical theories. Second, we extract the asymptotic parameter λ from simulation data with the statistical technique of robust regression. Robust regression is admirably suited to 'asymptotic regression' and deserves to be better known for it

  20. Policy implications for familial searching

    Directory of Open Access Journals (Sweden)

    Kim Joyce

    2011-11-01

    Full Text Available Abstract In the United States, several states have made policy decisions regarding whether and how to use familial searching of the Combined DNA Index System (CODIS database in criminal investigations. Familial searching pushes DNA typing beyond merely identifying individuals to detecting genetic relatedness, an application previously reserved for missing persons identifications and custody battles. The intentional search of CODIS for partial matches to an item of evidence offers law enforcement agencies a powerful tool for developing investigative leads, apprehending criminals, revitalizing cold cases and exonerating wrongfully convicted individuals. As familial searching involves a range of logistical, social, ethical and legal considerations, states are now grappling with policy options for implementing familial searching to balance crime fighting with its potential impact on society. When developing policies for familial searching, legislators should take into account the impact of familial searching on select populations and the need to minimize personal intrusion on relatives of individuals in the DNA database. This review describes the approaches used to narrow a suspect pool from a partial match search of CODIS and summarizes the economic, ethical, logistical and political challenges of implementing familial searching. We examine particular US state policies and the policy options adopted to address these issues. The aim of this review is to provide objective background information on the controversial approach of familial searching to inform policy decisions in this area. Herein we highlight key policy options and recommendations regarding effective utilization of familial searching that minimize harm to and afford maximum protection of US citizens.

  1. Attributes of Alignment of Real Estate and Facilities Management to Business Needs – an international comparative analysis

    DEFF Research Database (Denmark)

    Shiem-shin, Danny Then; Tan, Teng-hee; Santovito, Rogerio Fonseca;

    2014-01-01

    ”, being the most important criteria for the alignment between supply and demand of facility solutions in relation to business needs. One of the main differences in agreement was between the importance of strategy versus cost in the alignment between “facility solutions” and “FM services”. Originality....../value •Alignment of RE/FM to business needs is an essential management task and an important tool for RE/FM executives to create added value to their core business. However, there has so far only been limited research into such an alignment concept applicable to FM and an implementation model....

  2. A near-Infrared SETI Experiment: Alignment and Astrometric precision

    Science.gov (United States)

    Duenas, Andres; Maire, Jerome; Wright, Shelley; Drake, Frank D.; Marcy, Geoffrey W.; Siemion, Andrew; Stone, Remington P. S.; Tallis, Melisa; Treffers, Richard R.; Werthimer, Dan

    2016-06-01

    Beginning in March 2015, a Near-InfraRed Optical SETI (NIROSETI) instrument aiming to search for fast nanosecond laser pulses, has been commissioned on the Nickel 1m-telescope at Lick Observatory. The NIROSETI instrument makes use of an optical guide camera, SONY ICX694 CCD from PointGrey, to align our selected sources into two 200µm near-infrared Avalanche Photo Diodes (APD) with a field-of-view of 2.5"x2.5" each. These APD detectors operate at very fast bandwidths and are able to detect pulse widths extending down into the nanosecond range. Aligning sources onto these relatively small detectors requires characterizing the guide camera plate scale, static optical distortion solution, and relative orientation with respect to the APD detectors. We determined the guide camera plate scale as 55.9+- 2.7 milli-arcseconds/pixel and magnitude limit of 18.15mag (+1.07/-0.58) in V-band. We will present the full distortion solution of the guide camera, orientation, and our alignment method between the camera and the two APDs, and will discuss target selection within the NIROSETI observational campaign, including coordination with Breakthrough Listen.

  3. ALFRED: A Practical Method for Alignment-Free Distance Computation.

    Science.gov (United States)

    Thankachan, Sharma V; Chockalingam, Sriram P; Liu, Yongchao; Apostolico, Alberto; Aluru, Srinivas

    2016-06-01

    Alignment-free approaches are gaining persistent interest in many sequence analysis applications such as phylogenetic inference and metagenomic classification/clustering, especially for large-scale sequence datasets. Besides the widely used k-mer methods, the average common substring (ACS) approach has emerged to be one of the well-known alignment-free approaches. Two recent works further generalize this ACS approach by allowing a bounded number k of mismatches in the common substrings, relying on approximation (linear time) and exact computation, respectively. Albeit having a good worst-case time complexity [Formula: see text], the exact approach is complex and unlikely to be efficient in practice. Herein, we present ALFRED, an alignment-free distance computation method, which solves the generalized common substring search problem via exact computation. Compared to the theoretical approach, our algorithm is easier to implement and more practical to use, while still providing highly competitive theoretical performances with an expected run-time of [Formula: see text]. By applying our program to phylogenetic inference as a case study, we find that our program facilitates to exactly reconstruct the topology of the reference phylogenetic tree for a set of 27 primate mitochondrial genomes, at reasonably acceptable speed. ALFRED is implemented in C++ programming language and the source code is freely available online. PMID:27138275

  4. TECHNIQUES USED IN SEARCH ENGINE MARKETING

    OpenAIRE

    Assoc. Prof. Liviu Ion Ciora Ph. D; Lect. Ion Buligiu Ph. D

    2010-01-01

    Search engine marketing (SEM) is a generic term covering a variety of marketing techniques intended for attracting web traffic in search engines and directories. SEM is a popular tool since it has the potential of substantial gains with minimum investment. On the one side, most search engines and directories offer free or extremely cheap listing. On the other side, the traffic coming from search engines and directories tends to be motivated for acquisitions, making these visitors some of the ...

  5. Biosequence Similarity Search on the Mercury System

    OpenAIRE

    Krishnamurthy, Praveen; Buhler, Jeremy; Chamberlain, Roger; Franklin, Mark; Gyang, Kwame; Jacob, Arpith; Lancaster, Joseph

    2007-01-01

    Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high...

  6. SANSparallel: interactive homology search against Uniprot.

    Science.gov (United States)

    Somervuo, Panu; Holm, Liisa

    2015-07-01

    Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest. PMID:25855811

  7. Galaxy alignments: Observations and impact on cosmology

    CERN Document Server

    Kirk, Donnacha; Hoekstra, Henk; Joachimi, Benjamin; Kitching, Thomas D; Mandelbaum, Rachel; Sifón, Cristóbal; Cacciato, Marcello; Choi, Ami; Kiessling, Alina; Leonard, Adrienne; Rassat, Anais; Schäfer, Björn Malte

    2015-01-01

    Galaxy shapes are not randomly oriented, rather they are statistically aligned in a way that can depend on formation environment, history and galaxy type. Studying the alignment of galaxies can therefore deliver important information about the astrophysics of galaxy formation and evolution as well as the growth of structure in the Universe. In this review paper we summarise key measurements of intrinsic alignments, divided by galaxy type, scale and environment. We also cover the statistics and formalism necessary to understand the observations in the literature. With the emergence of weak gravitational lensing as a precision probe of cosmology, galaxy alignments took on an added importance because they can mimic cosmic shear, the effect of gravitational lensing by large-scale structure on observed galaxy shapes. This makes intrinsic alignments an important systematic effect in weak lensing studies. We quantify the impact of intrinsic alignments on cosmic shear surveys and finish by reviewing practical mitigat...

  8. Magnetic alignment and patterning of cellulose fibers

    International Nuclear Information System (INIS)

    The alignment and patterning of cellulose fibers under magnetic fields are reported. Static and rotating magnetic fields were used to align cellulose fibers with sizes ranging from millimeter to nanometer sizes. Cellulose fibers of the millimeter order, which were prepared for papermaking, and much smaller fibers with micrometer to nanometer sizes prepared by the acid hydrolysis of larger ones underwent magnetic alignment. Under a rotating field, a uniaxial alignment of fibers was achieved. The alignment was successfully fixed by the photopolymerization of a UV-curable resin precursor used as matrix. A monodomain chiral nematic film was prepared from an aqueous suspension of nanofibers. Using a field modulator inserted in a homogeneous magnetic field, simultaneous alignment and patterning were achieved

  9. Magnetic alignment and patterning of cellulose fibers

    Directory of Open Access Journals (Sweden)

    Fumiko Kimura and Tsunehisa Kimura

    2008-01-01

    Full Text Available The alignment and patterning of cellulose fibers under magnetic fields are reported. Static and rotating magnetic fields were used to align cellulose fibers with sizes ranging from millimeter to nanometer sizes. Cellulose fibers of the millimeter order, which were prepared for papermaking, and much smaller fibers with micrometer to nanometer sizes prepared by the acid hydrolysis of larger ones underwent magnetic alignment. Under a rotating field, a uniaxial alignment of fibers was achieved. The alignment was successfully fixed by the photopolymerization of a UV-curable resin precursor used as matrix. A monodomain chiral nematic film was prepared from an aqueous suspension of nanofibers. Using a field modulator inserted in a homogeneous magnetic field, simultaneous alignment and patterning were achieved

  10. Magnetic alignment and patterning of cellulose fibers

    Energy Technology Data Exchange (ETDEWEB)

    Kimura, Fumiko; Kimura, Tsunehisa [Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502 (Japan)], E-mail: tkimura@kais.kyoto-u.ac.jp

    2008-04-01

    The alignment and patterning of cellulose fibers under magnetic fields are reported. Static and rotating magnetic fields were used to align cellulose fibers with sizes ranging from millimeter to nanometer sizes. Cellulose fibers of the millimeter order, which were prepared for papermaking, and much smaller fibers with micrometer to nanometer sizes prepared by the acid hydrolysis of larger ones underwent magnetic alignment. Under a rotating field, a uniaxial alignment of fibers was achieved. The alignment was successfully fixed by the photopolymerization of a UV-curable resin precursor used as matrix. A monodomain chiral nematic film was prepared from an aqueous suspension of nanofibers. Using a field modulator inserted in a homogeneous magnetic field, simultaneous alignment and patterning were achieved.

  11. Innovative optical alignment technique for CMP wafers

    Science.gov (United States)

    Sugaya, Ayako; Kanaya, Yuho; Nakajima, Shinichi; Nagayama, Tadashi; Shiraishi, Naomasa

    2002-07-01

    Detecting position of the wafers such as after CMP process is critical theme of current and forthcoming IC manufacturing. The alignment system must be with high accuracy for any process. To satisfy such requirements, we have studied and analyzed factors that have made alignment difficult. From the result of the studies, we have developed new optical alignment techniques which improve the accuracy of FIA (alignment sensor of Nikon's NSR series) and examined them. The approaches are optimizing the focus position, developing an advanced algorithm for position detection, and selecting a suitable mark design. For experiment, we have developed the special wafers that make it possible to evaluate the influence of CMP processes. The experimental results show that the overlay errors decrease dramatically with the new alignment techniques. FIA with these new techniques will be much accurate and suitable alignment sensor for CMP and other processes of future generation ULSI production.

  12. Recursions for Statistical Multiple Alignment

    DEFF Research Database (Denmark)

    Hein, Jotun; Pedersen, Christian Nørgaard Storm; Jensen, Jens Ledet

    2002-01-01

    Algorithms are presented that allow the calculation of the probability of a set of sequences related by a binary tree that have evolved according to the Thorne–Kishino–Felsenstein model for a fixed set of parameters. The algorithms are based on a Markov chain generating sequences...... and their alignment at nodes in a tree. Depending on whether the complete realization of this Markov chain is decomposed into the first transition and the rest of the realization or the last transition and the first part of the realization, two kinds of recursions are obtained that are computationally similar...... but probabilistically different. The running time of the algorithms is , where Li is the length of the ith observed sequences and d is the number of sequences. An alternative recursion is also formulated that uses only a Markov chain involving the inner nodes of a tree....

  13. Scintillation counter: photomultiplier tube alignment

    International Nuclear Information System (INIS)

    A scintillation counter, particularly for counting gamma ray photons, includes a massive lead radiation shield surrounding a sample-receiving zone. The shield is disassembleable into a plurality of segments to allow facile installation and removal of a photomultiplier tube assembly, the segments being so constructed as to prevent straight-line access of external radiation through the shield into the sample receiving zone. Provisions are made for accurately aligning the photomultiplier tube with respect to one or more sample-transmitting bores extending through the shield to the sample receiving zone. A sample elevator, used in transporting samples into the zone, is designed to provide a maximum gamma-receiving aspect to maximize the gamma detecting efficiency. (auth)

  14. FUSE: Multiple Network Alignment via Data Fusion

    OpenAIRE

    Gligorijević, Vladimir; Malod-Dognin, Noël; Pržulj, Nataša

    2014-01-01

    Discovering patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. The objective of a multiple network alignment is to create clusters of nodes that are evolutionarily conserved and functionally consistent across all networks. Unfortunately, the alignment methods ...

  15. Measurement of alignment between standards and assessment

    OpenAIRE

    Näsström, Gunilla

    2008-01-01

    Many educational systems of today are standards-based and aim at for alignment, i.e. consistency, among the components of the educational system: standards, teaching and assessment. To conclude whether the alignment is sufficiently high, analyses with a useful model are needed. This thesis investigates the usefulness of models for analyzing alignment between standards and assessments, with emphasis on one method: Bloom’s revised taxonomy. The thesis comprises an introduction and five articles...

  16. Lower extremity alignment normogram of Turkish population

    OpenAIRE

    Sezen, Sedat; Kuyurtar, Fehmi; ERDOGAN, Murat; Karaoglanoglu, Mustafa

    2004-01-01

    Extremity alignment normogram is useful in planning arthroplasty, osteotomy and treatment of fracture and malunion. The aim of this study is to get a lower extremity alignment normogram of Turkish population. Lower extremity plain radiographs of a hundred healthy volunteer are obtained and 21 parameters are measured in each of them. Results are statistically analyzed. Mechanical factors depending on aging, alters lower extremity alignment normogram parameters in Turkish population. When lower...

  17. Overlay Alignment Using Two Photonic Crystals

    CERN Document Server

    Peng, C; Morton, K; Yu, Z; Chou, Stephen Y.; Morton, Keith; Peng, Can; Yu, Zhaoning

    2005-01-01

    In this paper we proposed a novel overlay alignment method using two sets of identical photonic crystals (PhCs). In this method the reflection or transmission spectrum of the two overlaid photonic crystals is measured to help wafer tilt, yaw rotation, and translation aligning. The initial testing results with two 1D photonic crystals and analysis of the alignment accuracy are presented. This method is particularly useful in building photonic crystal stacks with nanoimprint lithography (NIL).

  18. Project Lefty: More Bang for the Search Query

    Science.gov (United States)

    Varnum, Ken

    2010-01-01

    This article describes the Project Lefty, a search system that, at a minimum, adds a layer on top of traditional federated search tools that will make the wait for results more worthwhile for researchers. At best, Project Lefty improves search queries and relevance rankings for web-scale discovery tools to make the results themselves more relevant…

  19. Faceted Search

    CERN Document Server

    Tunkelang, Daniel

    2009-01-01

    We live in an information age that requires us, more than ever, to represent, access, and use information. Over the last several decades, we have developed a modern science and technology for information retrieval, relentlessly pursuing the vision of a "memex" that Vannevar Bush proposed in his seminal article, "As We May Think." Faceted search plays a key role in this program. Faceted search addresses weaknesses of conventional search approaches and has emerged as a foundation for interactive information retrieval. User studies demonstrate that faceted search provides more

  20. Are search committees really searching?

    Science.gov (United States)

    Hoffmeir, Patricia A

    2003-02-01

    Academic chair searches are admittedly a labor-intensive process, but they are made more difficult and often lead to less-than-optimal outcomes because search committees spend their time "advertising," "looking," but not truly searching for academic chairs. At the onset, certain "realities" must be acknowledged, including (1) understanding that unless your organization is renowned in the specialty for which you are conducting the search, candidates won't be pounding at your door for a job, (2) searches that fail to include an overall assessment of the department in question are likely to miss the mark, (3) chairs must have demonstrated not only clinical expertise but also business savvy, (4) the best candidate is not necessarily someone who is already a department chair, (5) when it comes to chair searches, it's a buyer's market, and (6) the search process is inextricably linked to the success of the search. Key to the process of conducting an academic chair search are the judicious formation of the search committee; committee members' willingness to do their homework, attend all committee meeting, and keep the committee's activities confidential; crafting, not revising, the current job description for the open chair position; interviewing viable candidates rather than all candidates and adhering to a coordinated interviewing process; and evaluating internal and external candidates according to the same parameters. PMID:12584089