Salt tectonics in an experimental turbiditic tank

Science.gov (United States)

Sellier, Nicolas; Vendeville, Bruno

2010-05-01

We modelled the effect of the deposition of clastic sediments wedges along passive margin by combining two different experimental approaches. The first approach, which uses flume experiments in order to model turbiditic transport and deposition, had focused, so far mainly on the stratigraphic architecture and flow properties. But most experiments have not accounted for the impact of syndepositional deformation. The second approach is the classic tectonic modelling (sand-box experiments) is aimed essentially at understanding deformation, for example the deformation of a sediment wedge deposited onto a mobile salt layer. However, with this approach, the sediment transport processes are crudely modelled by adding each sediment layer uniformly, regardless of the potential influence of the sea-floor bathymetry on the depositional pattern. We designed a new tectono-stratigraphic modelling tank, which combines modelling of the turbiditic transport and deposition, and salt-related deformation driven by sediment loading. The set-up comprises a channel connected to a main water tank. A deformation box is placed at the mouth of the channel, on the base of the tank. The base of the box can be filled with various kinds of substrates either rigid (sand) or viscous (silicone polymer, simulating mobile salt layer having varying length and thickness). A mixture of fine-grained powder and water is maintained in suspension in a container, and then released and channelled toward the basin, generating an analogue of basin-floor fans or lobes. We investigated the effect of depositing several consecutive turbiditic lobes on the deformation of the salt body and its overburden. The dynamics of experimental turbidity currents lead to deposits whose thickness varied gradually laterally: the lobe is thick in the proximal region and thins progressively distally, thus creating a very gentle regional surface slope. As the fan grows by episodic deposition of successive turbiditic lobes, the model

Great earthquakes along the Western United States continental margin: implications for hazards, stratigraphy and turbidite lithology

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C. H. Nelson

2012-11-01

Full Text Available We summarize the importance of great earthquakes (M_w ≳ 8 for hazards, stratigraphy of basin floors, and turbidite lithology along the active tectonic continental margins of the Cascadia subduction zone and the northern San Andreas Transform Fault by utilizing studies of swath bathymetry visual core descriptions, grain size analysis, X-ray radiographs and physical properties. Recurrence times of Holocene turbidites as proxies for earthquakes on the Cascadia and northern California margins are analyzed using two methods: (1 radiometric dating (¹⁴C method, and (2 relative dating, using hemipelagic sediment thickness and sedimentation rates (H method. The H method provides (1 the best estimate of minimum recurrence times, which are the most important for seismic hazards risk analysis, and (2 the most complete dataset of recurrence times, which shows a normal distribution pattern for paleoseismic turbidite frequencies. We observe that, on these tectonically active continental margins, during the sea-level highstand of Holocene time, triggering of turbidity currents is controlled dominantly by earthquakes, and paleoseismic turbidites have an average recurrence time of ~550 yr in northern Cascadia Basin and ~200 yr along northern California margin. The minimum recurrence times for great earthquakes are approximately 300 yr for the Cascadia subduction zone and 130 yr for the northern San Andreas Fault, which indicates both fault systems are in (Cascadia or very close (San Andreas to the early window for another great earthquake.

On active tectonic margins with great earthquakes, the volumes of mass transport deposits (MTDs are limited on basin floors along the margins. The maximum run-out distances of MTD sheets across abyssal-basin floors along active margins are an order of magnitude less (~100 km than on passive margins (~1000 km. The great earthquakes along the Cascadia and northern California margins

Controlling factors of stratigraphic occurrences of fine-grained turbidites: Examples from the Japanese waters

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Ikehara, K.

2017-12-01

Fine-grained turbidite has been used for subaqueous paleoseismology, and has been recognized from shallow- to deep-water environments around the Japanese islands. Stratigraphic occurrence of fine-grained turbidites in the deepest Beppu Bay, south Japan, with its water depth of 75 m suggest clear influence of sea-level changes. Turbidite frequency was high during the post glacial sea-level rising and last 2.7 ka, and was low during the Holocene maximum sea-level highstand (5.3-2.7 ka). Retreat and progress of coastal delta front of the nearby river might affect the sediment supply to the deepest basin. On the other hand, fine-grained turbidites found in the forearc basins ( 3500 and 4500 m in water depths) and trench floor ( 6000 m in water depth) along the southern Ryukyu arc have no clear relation with sea-level changes. Sediment and bathymetric characteristics suggest that origin of these fine-grained turbidites is Taiwan. Remarkable tectonic uplift of Taiwanese coast with small mountainous rivers and narrow shelf may produce the continuous supply of fine-grained turbidites in this area. The Japan Trench floor composes of a series of small basins reflecting subducting horst-graben structure of the Pacific Plate. Each small basin acts as a natural sediment trap receiving the earthquake-induced turbidity currents. Thick fine-grained turbidites are also occurred in the small basins in the Japan Trench floor ( 7500 m in water depth). These are most likely induced by huge earthquakes along the Japan Trench. Thus, their stratigraphic occurrences might have close relation with recurrence of huge earthquakes in the past.

Sedimentologic and Geometric Characterization of Turbidites of Brazos-Trinity Basin IV in the Gulf of Mexico: Preliminary Results of IODP Expedition 308

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Gutierrez-Pastor, J.; Pirmez, C.; Flemings, P. B.; Behrmann, J. H.; John, C. M.

2005-12-01

Brazos Trinity Basin IV is located about 200 km offshore Texas, and belongs to a linked system of four intra slope mini basins. Basin IV provides a type section to characterize turbidites in salt withdrawal mini-basins of the Gulf of Mexico. IODP Expedition 308 has cored and logged complete pre-fan and fan sequences that are clearly distinguished with high-resolution seismic profiles at Brazos Trinity Basin IV at Sites U1319, U1320 and U1321. Seismically imaged pre-fan and fan units also can be distinguished and correlated with the sedimentological and logging data. Turbidite facies display distinct properties in terms of grain size, bed thickness, color, organic matter content, vertical organization of beds and lateral distribution in all the units of the fan through the basin. The pre-fan sequence is composed of terrigenous laminated clay with color banding and it is interpreted to result from deposition from fluvial plumes and/or muddy turbidity currents overspilling from basins upstream of Basin IV. The lower fan is characterized by laminated and bioturbated muds with thin beds of silt and sand, and represent the initial infill of the basin by mostly muddy turbidity currents, although an exceptionally sand-rich unit occurs at the base of the lower fan. The middle and upper fan represent the main pulses of turbidity current influx into Basin IV, and contain fine to medium sand turbidite beds organized in packets ranging in thickness from 5 to 25 m. The middle fan displays an overall upward increase in sand content at Site U1320, suggesting increased flow by-pass from the updip basins through time. Key examples of turbidites from each fan unit are analysed in detail to infer the depositional processes and infilling history of Brazos-Trinity Basin IV. The study of turbidites in a calibrated basin such as Basin IV provides ground truth for the sedimentological processes and resultant seismic facies, which can be used to interpret the infill history of other

Multi-scale characterization of an upcurrent turbiditic pinch-out

Science.gov (United States)

Daghdevirenian, L. J. P.; Migeon, S.; Rubino, J. L., Sr.; Raisson, F.

2017-12-01

Continental margins with a steep topographic profile between their continental shelf and the basin exhibit a sudden slope break at the base of their continental slope. This slope break favors strong erosion or a by-pass and a fast accumulation of sediments on the base of the continental slope due to the hydraulic jump phenomena. Such a process is responsible for the construction of thick accumulations of limited extension and generally disconnected from the feeding tributaries. These accumulations usually onlap against the continental slope but their modality of pinch out is still questioned and it is the subject of this work. The Tabernas basin is located in South East of Spain, in the continuity of the Sorbas basin. Recent field works allowed identifying a "sedimentary" onlap associated with a small-scale sandy turbidite system that we discovered near the so-called El Buho area. The superb quality of the outcrops revealed, the presence of three successive onlap structures consisting in each case of a direct contact between fluvial conglomerates / marines conglomerates / marine marls / turbidite sands. Reconstruction of paleo-current direction gives a flow direction around N00, from north to south, suggesting the outcrops are cutting the pinch out of the sandy system in a longitudinal direction. A longitudinal and vertical transition of facies can be thus observed from marines' conglomerates to turbidite sands, respectively over distances of 500 m and 70 m. The complete evolution of facies along the pinch out consists of thick conglomerates in the proximal part to sandy turbidite channels then lobes in the distal part. The three successive onlap structures are located inside the channelize part of the system, just above a slope break structure. The basal units of the pinch out consist of an alternation of conglomerates and sandy bed, while the overlying units exhibits more sandy dominated beds. In order to reconstruct the architecture of the pinch out and to

Great earthquakes along the Western United States continental margin: implications for hazards, stratigraphy and turbidite lithology

Science.gov (United States)

Nelson, C. H.; Gutiérrez Pastor, J.; Goldfinger, C.; Escutia, C.

2012-11-01

We summarize the importance of great earthquakes (Mw ≳ 8) for hazards, stratigraphy of basin floors, and turbidite lithology along the active tectonic continental margins of the Cascadia subduction zone and the northern San Andreas Transform Fault by utilizing studies of swath bathymetry visual core descriptions, grain size analysis, X-ray radiographs and physical properties. Recurrence times of Holocene turbidites as proxies for earthquakes on the Cascadia and northern California margins are analyzed using two methods: (1) radiometric dating (14C method), and (2) relative dating, using hemipelagic sediment thickness and sedimentation rates (H method). The H method provides (1) the best estimate of minimum recurrence times, which are the most important for seismic hazards risk analysis, and (2) the most complete dataset of recurrence times, which shows a normal distribution pattern for paleoseismic turbidite frequencies. We observe that, on these tectonically active continental margins, during the sea-level highstand of Holocene time, triggering of turbidity currents is controlled dominantly by earthquakes, and paleoseismic turbidites have an average recurrence time of ~550 yr in northern Cascadia Basin and ~200 yr along northern California margin. The minimum recurrence times for great earthquakes are approximately 300 yr for the Cascadia subduction zone and 130 yr for the northern San Andreas Fault, which indicates both fault systems are in (Cascadia) or very close (San Andreas) to the early window for another great earthquake. On active tectonic margins with great earthquakes, the volumes of mass transport deposits (MTDs) are limited on basin floors along the margins. The maximum run-out distances of MTD sheets across abyssal-basin floors along active margins are an order of magnitude less (~100 km) than on passive margins (~1000 km). The great earthquakes along the Cascadia and northern California margins cause seismic strengthening of the sediment, which

Lowstand Turbidites and Delta Systems of the Itararé Group in the Vidal Ramos region (SC, southern Brazil

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Carla Gimena Puigdomenech

Full Text Available Turbidites have captioned the attention of sedimentologists during the last decades due their importance as hydrocarbon reservoirs. However, their relationship to delta systems still deserves further studies. This paper presents examples from a late deglacial to early post-glacial deltaic and turbidite strata exposed in the surroundings of Vidal Ramos (Santa Catarina State, Brazil, southern portion of the Paraná Basin. There, the uppermost part of the Mafra Formation and the Rio do Sul Formation onlap the Proterozoic basement and comprises an up to 360 m thick package. It includes (base to top black shales, mass transport deposits (MTD and sandy turbidites (Mafra Formation as well as thin bedded turbidites (tbt, including one interval of black shales and sandy turbidites, overlain by proximal delta front sandstones (Rio do Sul Formation. The analysis of the succession shows two more than 150 m thick coarsening-upwards deltaic successions composed of turbidite sand sheets at their base (prodelta, followed by partially collapsed thin bedded turbidites (delta slope wedge and delta front sandstones. Both turbidite sand-sheets abruptly overlay black shale intervals related to maximum flooding surfaces and therefore record correlative conformities. A detailed stratigraphic section elaborated from the correlation of four logs (1/100 suggests that distal delta front sands includes both thin bedded turbidites and wave reworked sands whereas the proximal delta front was dominated by long-lived underflows (hyperpycnal flows. The succession suggests that the most expressive turbidite beds (base of the delta systems have resulted from relative sea-level falls (early lowstand whereas the thin-bedded turbidites were related to the development of the late lowstand wedge. Black shales represent the transgressive systems tract and HST were not deposited or preserved in the area. High sediment supply associated with lowstand tracts could explain the occasional

Turbidites as proxy for past flood events: Testing this approach in a large clastic system (Lake Geneva, France/Switzerland)

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Kremer, Katrina; Girardclos, Stéphanie

2017-04-01

Turbidites recorded in lake sediments are often used to reconstruct the frequency of past flood and also seismological events. However, for such a reconstruction, the origin and causes of the recorded turbidites need to be clearly identified. In this study, we test if turbidites can be used as paleohydrological archive based on the the sedimentary record of Lake Geneva resulting from inputs by the Rhone and Dranse clastic river systems. Our approach is based on several methods combining high-resolution seismic reflection data with geophysical (magnetic susceptibility, grain size) and high-resolution XRF/XRD data measured on ca. 10-m-long sediment cores (dated by radiocarbon ages and 137Cs activity). This dataset allows distinguishing between the different sources (rivers or hemipelagic sediment) of the turbidites deposited in the deep basin of Lake Geneva. However, no clear distinction between the various trigger processes (mass failures or floods) could be made, thus flood deposits could not be clearly identified. From our results, we also conclude that the lack of turbidite deposits in the deep basin between the 15th and 18th century seems to be linked to a change in turbidite depocentre due to the Rhone River mouth shifting possibly triggered by human activity and not by any direct climate effect. This study demonstrates that a least two conditions are needed to perform an adequate paleohydrological interpretation based on turbidite records: (1) the holistic understanding of the basin sedimentary system and (2) the distinction of flood-induced turbidites from other types of turbidites (mass failures etc.).

Provenance analysis of the Oligocene turbidites (Andaman Flysch ...

Indian Academy of Sciences (India)

d. F. L. L. L. P. P. Figure 2. Field photographs of the Andaman Flysch turbidites. ... sandstone bed and produce flame (F) structures; (e) A variety of sole marks at the base of an ...... Nicobar: The Neogene; Capital Publishing Company, New.

Slipstream: an early Holocene slump and turbidite record from the frontal ridge of the Cascadia accretionary wedge off western Canada and paleoseismic implications

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Hamilton, T.S.; Enkin, Randolph J.; Riedel, Michael; Rogers, Gary C.; Pohlman, John W.; Benway, Heather M.

2015-01-01

Slipstream Slump, a well-preserved 3 km wide sedimentary failure from the frontal ridge of the Cascadia accretionary wedge 85 km off Vancouver Island, Canada, was sampled during Canadian Coast Guard Ship (CCGS) John P. Tully cruise 2008007PGC along a transect of five piston cores. Shipboard sediment analysis and physical property logging revealed 12 turbidites interbedded with thick hemipelagic sediments overlying the slumped glacial diamict. Despite the different sedimentary setting, atop the abyssal plain fan, this record is similar in number and age to the sequence of turbidites sampled farther to the south from channel systems along the Cascadia Subduction Zone, with no extra turbidites present in this local record. Given the regional physiographic and tectonic setting, megathrust earthquake shaking is the most likely trigger for both the initial slumping and subsequent turbidity currents, with sediments sourced exclusively from the exposed slump face of the frontal ridge. Planktonic foraminifera picked from the resedimented diamict of the underlying main slump have a disordered cluster of 14C ages between 12.8 and 14.5 ka BP. For the post-slump stratigraphy, an event-free depth scale is defined by removing the turbidite sediment intervals and using the hemipelagic sediments. Nine14C dates from the most foraminifera-rich intervals define a nearly constant hemipelagic sedimentation rate of 0.021 cm/year. The combined age model is defined using only planktonic foraminiferal dates and Bayesian analysis with a Poisson-process sedimentation model. The age model of ongoing hemipelagic sedimentation is strengthened by physical property correlations from Slipstream events to the turbidites for the Barkley Canyon site 40 km south. Additional modelling addressed the possibilities of seabed erosion or loss and basal erosion beneath turbidites. Neither of these approaches achieves a modern seabed age when applying the commonly used regional marine 14C reservoir age of

Non-cohesive silt turbidity current flow processes; insights from proximal sandy-silt and silty-sand turbidites, Fiordland, New Zealand

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Strachan, Lorna J.; Bostock, Helen C.; Barnes, Philip M.; Neil, Helen L.; Gosling, Matthew

2016-08-01

Silt-rich turbidites are commonly interpreted as distal marine deposits. They are associated with interlaminated clay and silt deposition from the upper and rear portions of turbidity currents. Here, multibeam bathymetry and shallow sediment core data from the intra-slope Secretary Basin, Fiordland, New Zealand, located laminar) flows that have undergone a variety of up-dip flow transformations. Most flows were initially erosive followed by deposition of partitioned 2- or 3- phase mixed mode flows that include high-density transitional and laminar flows that can be fore- or after-runners to low-density turbulent flow sections. Turbulence is inferred to have been suppressed in high-density flows by increasing flow concentration of both sands and silts. The very fine and fine sand modal grain sizes of sandy-silt and silty-sand turbidites are significantly coarser than classical abyssal plain silt turbidites and are generally coarser than overbank silt turbidites. While the low percentage of clays within Secretary Basin sandy-silt and silty-sand turbidites represents a fundamental difference between these and other silt and mud turbidites, we suggest these beds represent a previously undescribed suite of proximal continental slope deposits.

Quantitative estimation of lithofacies from seismic data in a tertiary turbidite system in the North Sea

Energy Technology Data Exchange (ETDEWEB)

Joerstad, A.K.; Avseth, P.Aa; Mukerji, T.; Mavko, G.; Granli, J.R.

1998-12-31

Deep water clastic systems and associated turbidite reservoirs are often characterized by very complex sand distributions and reservoir description based on conventional seismic and well-log stratigraphic analysis may be very uncertain in these depositional environments. There is shown that reservoirs in turbidite systems have been produced very inefficiently in conventional development. More than 70% of the mobile oil is commonly left behind, because of the heterogeneous nature of these reservoirs. In this study there is examined a turbidite system in the North Sea with five available wells and a 3-D seismic near and far offset stack to establish most likely estimates of facies and pore fluid within the cube. 5 figs.

Reservoir evaluation of thin-bedded turbidites and hydrocarbon pore thickness estimation for an accurate quantification of resource

Science.gov (United States)

Omoniyi, Bayonle; Stow, Dorrik

2016-04-01

One of the major challenges in the assessment of and production from turbidite reservoirs is to take full account of thin and medium-bedded turbidites (succession, they can go unnoticed by conventional analysis and so negatively impact on reserve estimation, particularly in fields producing from prolific thick-bedded turbidite reservoirs. Field development plans often take little note of such thin beds, which are therefore bypassed by mainstream production. In fact, the trapped and bypassed fluids can be vital where maximising field value and optimising production are key business drivers. We have studied in detail, a succession of thin-bedded turbidites associated with thicker-bedded reservoir facies in the North Brae Field, UKCS, using a combination of conventional logs and cores to assess the significance of thin-bedded turbidites in computing hydrocarbon pore thickness (HPT). This quantity, being an indirect measure of thickness, is critical for an accurate estimation of original-oil-in-place (OOIP). By using a combination of conventional and unconventional logging analysis techniques, we obtain three different results for the reservoir intervals studied. These results include estimated net sand thickness, average sand thickness, and their distribution trend within a 3D structural grid. The net sand thickness varies from 205 to 380 ft, and HPT ranges from 21.53 to 39.90 ft. We observe that an integrated approach (neutron-density cross plots conditioned to cores) to HPT quantification reduces the associated uncertainties significantly, resulting in estimation of 96% of actual HPT. Further work will focus on assessing the 3D dynamic connectivity of the low-pay sands with the surrounding thick-bedded turbidite facies.

Turbidite pathways in Cascadia Basin and Tufts abyssal plain, Part A, Astoria Channel, Blanco Valley, and Gorda Basin

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Wolf, Stephen C.; Hamer, Michael R.

1999-01-01

This open-file report was prepared in support of the USGS Earthquake Hazards of Cascadia Project. The primary objective of this phase of the project is to determine recurrence intervals of turbidites in Cascadia basin-floor channel systems and evaluate implications of this event record for the paleoseismic history of the Cascadia subduction zone. The purpose of this study is to determine whether the canyon/channel systems themselves are blocked or deformed in such a way that the downstream turbidite stratigraphy might be biased. To accomplish this investigation approximately 7500 kilometers of pre-existing 3.5 KHz seismic data were evaluated to determine the direction and extent of the Astoria Channel/pathway system, which originates at the base of the Astoria Fan. Additionally, distribution and thickness of turbidite sediment sequences were determined along each identified pathway. Bathymetery and distance were used to determine gradients along the main pathway axis and for each of the secondary pathways that feed into it. Channel pathways were identified on the basis of channel phyisiography, where visible at the seafloor, subbottom channel configuration, and acoustic packets of sediments that might represent turbidite deposits. A principal result of this study is that the Astoria Channel/pathway extends continuously from the base of the Astoria Fan southward along the base of the continental slope through the Blanco Valley, then heads southwestward through the Gorda Basin and into the region of the Escanaba Trough. Additionally it was determined that the Astoria Channel is filled and basically buried for it's full length south of 44 degrees latitude. The 44 North Slump, as defined by Goldfinger (1999, see Map 3 ref.), may have been instrumental in blocking the pathway and thus contributed to the filling of the channel/pathway. Sheets 1 and 2 show the Astoria and secondary turbidite pathways highlighted in blue. Ship survey tracklines are shown for the area

Ooid turbidites from the Central Western continental margin of India

Digital Repository Service at National Institute of Oceanography (India)

Rao, P.S.

Gravity displaced debris flows/turbidites have been observed in five box cores collected between water depths of 649 and 3,627 m from the Central Western continental margin of India. Studies on grain size, carbonate content, and coarse fraction...

Paleoseismology under sea: First evidence for irregular seismic cycles during Holocene off Algeria from turbidites

Science.gov (United States)

Ratzov, Gueorgui; Cattaneo, Antonio; Babonneau, Nathalie; Déverchere, Jacques; Yelles, Karim; Bracene, Rabah

2013-04-01

According to simple models, stress build-up along a given fault is proportional to the time elapsed since the previous earthquake. Although the resulting « seismic gap » hypothesis suits well for moderate magnitude earthquake (Mw 4-5), large events (Mw>6) are hardly predictable and show great variation in recurrence intervals. Thus, models based on stress transfer and interactions between faults suggest that an earthquake may haste or delay the occurrence of next earthquake on adjacent fault by increasing or lowering the level of static stress. Here, we show that meaningful information of large earthquakes recurrence intervals over several seismic cycles may be obtained using turbidite record offshore the Algerian margin (Mediterranean Sea), an area prone to relatively large (M~7) earthquakes in historical times. Indeed, as evidenced on the Cascadia subduction zone, synchroneous turbidites over a large area and originated from independent sources, are most likely triggered by an earthquake. To test the method on this slowly convergent margin, we analysed turbidites in 3 sediment cores collected off the area shaken by the 1980 Ms 7.3 El Asnam and 1954 M6.7 Orléansville earthquakes. We used X-ray radioscopy, XRF major elements counter, magnetic susceptibility, and grain-size distribution to accurately discriminate turbidites (~instantaneous deposit) from hemipelagites (continuous background sedimentation). We dated turbidites by calculating hemipelagic sedimentation rates obtained with AMS radiocarbon ages, and applied the rates between turbidites. Finally, the age of events was compared to the only paleoseismic investigation available onland. We found that 10 to 25 turbidites deposited as single or multiple pulses over the last ~8ka. Once correlated from site to site, they support 14 seismic events. Most events are correlated with the paleoseismic record of the El Asnam fault, but uncorrelated events support that other faults were active. Only the first of the

Turbidites and Benthic Faunal Succession in the Deep Sea: An Ecological Paradox

National Research Council Canada - National Science Library

Young, David

2001-01-01

Characteristics of benthic faunal succession following turbidity flows in the deep sea will vary according to the composition of turbidite materials, the spatial scales of deposition, the structure...

Flow dynamics at the origin of thin clayey sand lacustrine turbidites: Examples from Lake Hazar, Turkey

KAUST Repository

Hage, Sophie

2017-04-18

Turbidity currents and their deposits can be investigated using several methods, i.e. direct monitoring, physical and numerical modelling, sediment cores and outcrops. The present study focuses on thin clayey sand turbidites found in Lake Hazar (Turkey) occurring in eleven clusters of closely spaced thin beds. Depositional processes and sources for three of those eleven clusters are studied at three coring sites. Bathymetrical data and seismic reflection profiles are used to understand the specific geomorphology of each site. X-ray, thin sections and CT-scans imagery combined with grain-size, geochemical and mineralogical measurements on the cores allow characterisation of the turbidites. Turbidites included in each cluster were produced by remobilization of surficial slope sediment, a process identified in very few studies worldwide. Three types of turbidites are distinguished and compared with deposits obtained in flume studies published in the literature. Type 1 is made of an ungraded clayey silt layer issued from a cohesive flow. Type 2 is composed of a partially graded clayey sand layer overlain by a mud cap, attributed to a transitional flow. Type 3 corresponds to a graded clayey sand layer overlain by a mud cap issued from a turbulence-dominated flow. While the published experimental studies show that turbulence is damped by cohesion for low clay content, type 3 deposits of this study show evidence for a turbulence dominated mechanism despite their high clay content. This divergence may in part relate to input variables such as water chemistry and clay mineralogy that are not routinely considered in experimental studies. Furthermore, the large sedimentological variety observed in the turbidites from one coring site to another is related to the evolution of a sediment flow within a field scale basin made of a complex physiography that cannot be tackled by flume experiments.

Source to Sink Tectonic Fate of Large Oceanic Turbidite Systems and the Rupturing of Great and Giant Megathrust Earthquakes (Invited)

Science.gov (United States)

Scholl, D. W.; Kirby, S. H.; von Huene, R.

2010-12-01

OCEAN FLOOR OBSERVATIONS: Oceanic turbidite systems accumulate above igneous oceanic crust and are commonly huge in areal and volumetric dimensions. For example, the volume of the Zodiac fan of the Gulf of Alaska is roughly 300,000 cubic km. Other large oceanic systems construct the Amazon cone, flood the Bay of Bengal abyss, and accumulate along trench axes to thickness of 1 to 7 km and lengths of 1000 to 3000 km, e.g., the Aleutian-Alaska, Sumatra-Andaman, Makran, and south central Chile Trenches. THE ROCK RECORD: Despite the large dimensions of oceanic turbidite systems, they are poorly preserved in the rock record. This includes oceanic systems deposited in passive-margin oceans, e.g., the Paleozoic Iapetus and Rheric oceans of the Atlantic realm, This circumstance does not apply to Cretaceous and E. Tertiary rock sequences of the north Pacific rim where oceanic turbidite deposits are preserved as accretionary complexes, e.g., the Catalina-Pelona-Orocopia-Rand schist of California and the Chugach-Kodiak complex of Alaska. These rock bodies are exhumed crustal underplates of once deeply (15-30 km) subducted oceanic turbidite systems. PATH FROM SOURCE TO TECTONIC SINK: The fate of most oceanic turbidite systems is to be removed from the sea floor and, ultimately, destroyed. This circumstance is unavoidable because most of them are deposited on lower plate crust destined for destruction in a subduction zone. During the past 4-5 myr alone a volume of 1-1.5 million cubic km of sediment sourced from the glaciated drainages of the Gulf of Alaska flooded the 3000-km-long Aleutian-Alaska trench axis. A small part of this volume accumulated tectonically as a narrow, 10-30-km wide accretionary frontal prism. But about 80 percent was subducted and entered the subduction channel separating the two plates. The subduction channel, roughly 1 km thick, conveys the trench turbidite deposits landward down dip along the rupturing width of the seismogenic zone. SEISMIC CONSEQUENCE

Deep-water turbidites as Holocene earthquake proxies: the Cascadia subduction zone and Northern San Andreas Fault systems

Directory of Open Access Journals (Sweden)

J. E. Johnson

2003-06-01

Full Text Available New stratigraphic evidence from the Cascadia margin demonstrates that 13 earthquakes ruptured the margin from Vancouver Island to at least the California border following the catastrophic eruption of Mount Mazama. These 13 events have occurred with an average repeat time of ?? 600 years since the first post-Mazama event ?? 7500 years ago. The youngest event ?? 300 years ago probably coincides with widespread evidence of coastal subsidence and tsunami inundation in buried marshes along the Cascadia coast. We can extend the Holocene record to at least 9850 years, during which 18 events correlate along the same region. The pattern of repeat times is consistent with the pattern observed at most (but not all localities onshore, strengthening the contention that both were produced by plate-wide earthquakes. We also observe that the sequence of Holocene events in Cascadia may contain a repeating pattern, a tantalizing look at what may be the long-term behavior of a major fault system. Over the last ?? 7500 years, the pattern appears to have repeated at least three times, with the most recent A.D. 1700 event being the third of three events following a long interval of 845 years between events T4 and T5. This long interval is one that is also recognized in many of the coastal records, and may serve as an anchor point between the offshore and onshore records. Similar stratigraphic records are found in two piston cores and one box core from Noyo Channel, adjacent to the Northern San Andreas Fault, which show a cyclic record of turbidite beds, with thirty- one turbidite beds above a Holocene/.Pleistocene faunal «datum». Thus far, we have determined ages for 20 events including the uppermost 5 events from these cores. The uppermost event returns a «modern» age, which we interpret is likely the 1906 San Andreas earthquake. The penultimate event returns an intercept age of A.D. 1664 (2 ?? range 1505- 1822. The third event and fourth event

Late Cambrian - Early Ordovician turbidites of Gorny Altai (Russia): Compositions, sources, deposition settings, and tectonic implications

Science.gov (United States)

Kruk, Nikolai N.; Kuibida, Yana V.; Shokalsky, Sergey P.; Kiselev, Vladimir I.; Gusev, Nikolay I.

2018-06-01

The Cambrian-Ordovician transition was the time of several key events in the history of Central Asia. They were the accretion of Mariana-type island arc systems to the Siberian continent, the related large-scale orogeny and intrusions of basaltic and granitic magma and the formation of a huge turbidite basin commensurate with the Bengal Gulf basin in the western part of the Central Asian orogenic belt (CAOB). The structure of the basin, as well as the sources and environments of deposition remain open to discussion. This paper presents new major- and trace-element data on Late-Cambrian-Early Ordovician turbidites from different parts of the Russian Altai and a synthesis of Nd isotope composition and ages of detrital zircons. The turbidites share chemical similarity with material shed from weathered continental arcs. Broad variations of CIA (39-73) and ICV (0.63-1.66) signatures in sandstones suggest origin from diverse sources and absence of significant sorting. Trace elements vary considerably and have generally similar patterns in rocks from different terranes. On the other hand, there are at least two provinces according to Nd isotope composition and age of detrital zircons. Samples from eastern Russian Altai contain only Phanerozoic zircons and have Nd isotope ratios similar to those in Early Cambrian island arcs (εNdt + 4.4… + 5.4; TNd(DM)-2-st = 0.8-0.9 Ga). Samples from central, western, and southern parts of Russian Altai contain Precambrian zircons (some as old as Late Archean) and have a less radiogenic Nd composition (εNdt up to -3.6; TNd(DM)-2-st up to 1.5 Ga). The chemical signatures of Late Cambrian to Early Ordovician turbidites indicate a provenance chemically more mature than the island arc rocks, and the presence of zircons with 510-490 Ma ages disproves their genetic relation with island arcs. The turbidite basin formed simultaneously with peaks of granitic and alkali-basaltic magmatism in the western Central Asian orogen and resulted from

Differentiating submarine channel-related thin-bedded turbidite facies: Outcrop examples from the Rosario Formation, Mexico

Science.gov (United States)

Hansen, Larissa; Callow, Richard; Kane, Ian; Kneller, Ben

2017-08-01

Thin-bedded turbidites deposited by sediment gravity flows that spill from submarine channels often contain significant volumes of sand in laterally continuous beds. These can make up over 50% of the channel-belt fill volume, and can thus form commercially important hydrocarbon reservoirs. Thin-bedded turbidites can be deposited in environments that include levees and depositional terraces, which are distinguished on the basis of their external morphology and internal architecture. Levees have a distinctive wedge shaped morphology, thinning away from the channel, and confine both channels (internal levees) and channel-belts (external levees). Terraces are flat-lying features that are elevated above the active channel within a broad channel-belt. Despite the ubiquity of terraces and levees in modern submarine channel systems, the recognition of these environments in outcrop and in the subsurface is challenging. In this outcrop study of the Upper Cretaceous Rosario Formation (Baja California, Mexico), lateral transects based on multiple logged sections of thin-bedded turbidites reveal systematic differences in sandstone layer thicknesses, sandstone proportion, palaeocurrents, sedimentary structures and ichnology between channel-belt and external levee thin-bedded turbidites. Depositional terrace deposits have a larger standard deviation in sandstone layer thicknesses than external levees because they are topographically lower, and experience a wider range of turbidity current sizes overspilling from different parts of the channel-belt. The thickness of sandstone layers within external levees decreases away from the channel-belt while those in depositional terraces are less laterally variable. Depositional terrace environments of the channel-belt are characterized by high bioturbation intensities, and contain distinctive trace fossil assemblages, often dominated by ichnofabrics of the echinoid trace fossil Scolicia. These assemblages contrast with the lower

Deep-Sea Turbidites as Guides to Holocene Earthquake History at the Cascadia Subduction Zone—Alternative Views for a Seismic-Hazard Workshop

Science.gov (United States)

Atwater, Brian F.; Griggs, Gary B.

2012-01-01

This report reviews the geological basis for some recent estimates of earthquake hazards in the Cascadia region between southern British Columbia and northern California. The largest earthquakes to which the region is prone are in the range of magnitude 8-9. The source of these great earthquakes is the fault down which the oceanic Juan de Fuca Plate is being subducted or thrust beneath the North American Plate. Geologic evidence for their occurrence includes sedimentary deposits that have been observed in cores from deep-sea channels and fans. Earthquakes can initiate subaqueous slumps or slides that generate turbidity currents and which produce the sedimentary deposits known as turbidites. The hazard estimates reviewed in this report are derived mainly from deep-sea turbidites that have been interpreted as proxy records of great Cascadia earthquakes. The estimates were first published in 2008. Most of the evidence for them is contained in a monograph now in press. We have reviewed a small part of this evidence, chiefly from Cascadia Channel and its tributaries, all of which head offshore the Pacific coast of Washington State. According to the recent estimates, the Cascadia plate boundary ruptured along its full length in 19 or 20 earthquakes of magnitude 9 in the past 10,000 years; its northern third broke during these giant earthquakes only, and southern segments produced at least 20 additional, lesser earthquakes of Holocene age. The turbidite case for full-length ruptures depends on stratigraphic evidence for simultaneous shaking at the heads of multiple submarine canyons. The simultaneity has been inferred primarily from turbidite counts above a stratigraphic datum, sandy beds likened to strong-motion records, and radiocarbon ages adjusted for turbidity-current erosion. In alternatives proposed here, this turbidite evidence for simultaneous shaking is less sensitive to earthquake size and frequency than previously thought. Turbidites far below a channel

Upslope deposition of extremely distal turbidites: An example from the Tiburon Rise, west-central Atlantic

Science.gov (United States)

Dolan, James; Beck, Christian; Ogawa, Yujiro

1989-11-01

Terrigenous silt and sand turbidites recovered from the crest of the Tiburon Rise in the west-central Atlantic represent an unprecedented example of upslope turbidite deposition in an extremely distal setting. These Eocene-Oligocene beds, which were derived from South America more than 1000 km to the southeast, were probably deposited by extremely thick (>1500 m) turbidity currents that flowed parallel to the southern margin of the rise. We suggest that flow thickness was the dominant control on deposition of these beds, rather than true upslope flow. This interpretation points out the importance of local bathymetry on the behavior of even extremely distal turbidity currents.

Eye and sheath folds in turbidite convolute lamination: Aberystwyth Grits Group, Wales

Science.gov (United States)

McClelland, H. L. O.; Woodcock, N. H.; Gladstone, C.

2011-07-01

Eye and sheath folds are described from the turbidites of the Aberystwyth Group, in the Silurian of west Wales. They have been studied at outcrop and on high resolution optical scans of cut surfaces. The folds are not tectonic in origin. They occur as part of the convolute-laminated interval of each sand-mud turbidite bed. The thickness of this interval is most commonly between 20 and 100 mm. Lamination patterns confirm previous interpretations that convolute lamination nucleated on ripples and grew during continued sedimentation of the bed. The folds amplified vertically and were sheared horizontally by continuing turbidity flow, but only to average values of about γ = 1. The strongly curvilinear fold hinges are due not to high shear strains, but to nucleation on sinuous or linguoid ripples. The Aberystwyth Group structures provide a warning that not all eye folds in sedimentary or metasedimentary rocks should be interpreted as sections through high shear strain sheath folds.

Continental Growth and Recycling in Convergent Orogens with Large Turbidite Fans on Oceanic Crust

Directory of Open Access Journals (Sweden)

Ben D. Goscombe

2013-07-01

Full Text Available Convergent plate margins where large turbidite fans with slivers of oceanic basement are accreted to continents represent important sites of continental crustal growth and recycling. Crust accreted in these settings is dominated by an upper layer of recycled crustal and arc detritus (turbidites underlain by a layer of tectonically imbricated upper oceanic crust and/or thinned continental crust. When oceanic crust is converted to lower continental crust it represents a juvenile addition to the continental growth budget. This two-tiered accreted crust is often the same thickness as average continental crustal and is isostatically balanced near sea level. The Paleozoic Lachlan Orogen of eastern Australia is the archetypical example of a tubidite-dominated accretionary orogeny. The Neoproterozoic-Cambrian Damaran Orogen of SW Africa is similar to the Lachlan Orogen except that it was incorporated into Gondwana via a continent-continent collision. The Mesozoic Rangitatan Orogen of New Zealand illustrates the transition of convergent margin from a Lachlan-type to more typical accretionary wedge type orogen. The spatial and temporal variations in deformation, metamorphism, and magmatism across these orogens illustrate how large volumes of turbidite and their relict oceanic basement eventually become stable continental crust. The timing of deformation and metamorphism recorded in these rocks reflects the crustal thickening phase, whereas post-tectonic magmatism constrains the timing of chemical maturation and cratonization. Cratonization of continental crust is fostered because turbidites represent fertile sources for felsic magmatism. Recognition of similar orogens in the Proterozoic and Archean is important for the evaluation of crustal growth models, particularly for those based on detrital zircon age patterns, because crustal growth by accretion of upper oceanic crust or mafic underplating does not readily result in the addition of voluminous zircon

Stratigraphic and structural compartmentalization observed within a model turbidite reservoir, Pennsylvanian Upper Jackfork Formation, Hollywood Quarry, Arkansas

Energy Technology Data Exchange (ETDEWEB)

Slatt, R. [Colorado School of Mines, Golden, CO (United States); Jordan, D. [Arco International Oil and Gas Co., Plano, TX (United States); Stone, C. [Arkansas Geological Commission, Little Rock, AR (United States)] [and others

1995-08-01

Hollywood Quarry is a 600 x 375 x 150 ft. (200 x 125 x 50m) excavation which provides a window into lower Pennsylvanian Jackfork Formation turbidite stratal architecture along the crest of a faulted anticlinal fold. A variety of turbidite facies are present, including: (a) lenticular, channelized sandstones, pebbly sandstones, and conglomerates within shale, (b) laterally continuous, interbedded thin sandstones and shales, and (c) thicker, laterally continuous shales. The sandstone and shale layers we broken by several strike-slip and reverse faults, with vertical displacements of up to several feet. This combination of facies and structural elements has resulted in a highly compartmentalized stratigraphic interval, both horizontally and vertically, along the anticlinal flexure. The quarry can be considered analogous to a scaled-down turbidite reservoir. Outcrop gamma-ray logs, measured sections, a fault map, and cross sections provide a database which is analogous to what would be available for a subsurface reservoir. Thus, the quarry provides an ideal outdoor geologic and engineering {open_quote}workshop{close_quote} venue for visualizing the potential complexities of a combination structural-stratigraphic (turbidite) reservoir. Since all forms of compartmentalization are readily visible in the quarry, problems related to management of compartmentalized reservoirs can be discussed and analyzed first-hand while standing in the quarry, within this {open_quote}model reservoir{close_quotes}. These problems include: (a) the high degree of stratigraphic and structural complexity that may be encountered, even at close well spacings, (b) uncertainty in well log correlations and log-shape interpretations, (c) variations in volumetric calculations as a function of amount of data available, and (d) potential production problems associated with specific {open_quote}field{close_quote} development plans.

Enhanced Seismic Imaging of Turbidite Deposits in Chicontepec Basin, Mexico

Science.gov (United States)

Chavez-Perez, S.; Vargas-Meleza, L.

2007-05-01

We test, as postprocessing tools, a combination of migration deconvolution and geometric attributes to attack the complex problems of reflector resolution and detection in migrated seismic volumes. Migration deconvolution has been empirically shown to be an effective approach for enhancing the illumination of migrated images, which are blurred versions of the subsurface reflectivity distribution, by decreasing imaging artifacts, improving spatial resolution, and alleviating acquisition footprint problems. We utilize migration deconvolution as a means to improve the quality and resolution of 3D prestack time migrated results from Chicontepec basin, Mexico, a very relevant portion of the producing onshore sector of Pemex, the Mexican petroleum company. Seismic data covers the Agua Fria, Coapechaca, and Tajin fields. It exhibits acquisition footprint problems, migration artifacts and a severe lack of resolution in the target area, where turbidite deposits need to be characterized between major erosional surfaces. Vertical resolution is about 35 m and the main hydrocarbon plays are turbidite beds no more than 60 m thick. We also employ geometric attributes (e.g., coherent energy and curvature), computed after migration deconvolution, to detect and map out depositional features, and help design development wells in the area. Results of this workflow show imaging enhancement and allow us to identify meandering channels and individual sand bodies, previously undistinguishable in the original seismic migrated images.

Submarine paleoseismology based on turbidite records.

Science.gov (United States)

Goldfinger, Chris

2011-01-01

Many of the largest earthquakes are generated at subduction zones or other plate boundary fault systems near enough to the coast that marine environments may record evidence of them. During and shortly after large earthquakes in the coastal and marine environments, a spectrum of evidence may be left behind, mirroring onshore paleoseismic evidence. Shaking or displacement of the seafloor can trigger processes such as turbidity currents, submarine landslides, tsunami (which may be recorded both onshore and offshore), and soft-sediment deformation. Marine sites may also share evidence of fault scarps, colluvial wedges, offset features, and liquefaction or fluid expulsion with their onshore counterparts. This article reviews the use of submarine turbidite deposits for paleoseismology, focuses on the dating and correlation techniques used to establish stratigraphic continuity of marine deposits, and outlines criteria for distinguishing earthquake deposits and the strategies used to acquire suitable samples and data for marine paleoseismology.

Seismic architecture and lithofacies of turbidites in Lake Mead (Arizona and Nevada, U.S.A.), an analogue for topographically complex basins

Science.gov (United States)

Twichell, D.C.; Cross, V.A.; Hanson, A.D.; Buck, B.J.; Zybala, J.G.; Rudin, M.J.

2005-01-01

Turbidites, which have accumulated in Lake Mead since completion of the Hoover Dam in 1935, have been mapped using high-resolution seismic and coring techniques. This lake is an exceptional natural laboratory for studying fine-grained turbidite systems in complex topographic settings. The lake comprises four relatively broad basins separated by narrow canyons, and turbidity currents run the full length of the lake. The mean grain size of turbidites is mostly coarse silt, and the sand content decreases from 11-30% in beds in the easternmost basin nearest the source to 3-14% in the central basins to 1-2% in the most distal basin. Regionally, the seismic amplitude mimics the core results and decreases away from the source. The facies and morphology of the sediment surface varies between basins and suggests a regional progression from higher-energy and possibly channelized flows in the easternmost basin to unchannelized flows in the central two basins to unchannelized flows that are ponded by the Hoover Dam in the westernmost basin. At the local scale, turbidites are nearly flat-lying in the central two basins, but here the morphology of the basin walls strongly affects the distribution of facies. One of the two basins is relatively narrow, and in sinuous sections reflection amplitude increases toward the outsides of meanders. Where a narrow canyon debouches into a broad basin, reflection amplitude decreases radially away from the canyon mouth and forms a fan-like deposit. The fine-grained nature of the turbidites in the most distal basin and the fact that reflections drape the underlying pre-impoundment surface suggest ponding here. The progression from ponding in the most distal basin to possibly channelized flows in the most proximal basin shows in plan view a progression similar to the stratigraphic progression documented in several minibasins in the Gulf of Mexico. Copyright ?? 2005, SEPM (Society for Sedimentary Geology).

Flow dynamics at the origin of thin clayey sand lacustrine turbidites: Examples from Lake Hazar, Turkey

KAUST Repository

Hage, Sophie; Hubert-Ferrari, Auré lia; Lamair, Laura; Avsar, Ulas; El Ouahabi, Meriam; Van Daele, Maarten; Boulvain, Fré dé ric; Ali Bahri, Mohamed; Seret, Alain; Plenevaux, Alain

2017-01-01

relate to input variables such as water chemistry and clay mineralogy that are not routinely considered in experimental studies. Furthermore, the large sedimentological variety observed in the turbidites from one coring site to another is related

Frequency and sources of basin floor turbidites in alfonso basin, Gulf of California, Mexico: Products of slope failures

Science.gov (United States)

Gonzalez-Yajimovich, Oscar E.; Gorsline, Donn S.; Douglas, Robert G.

2007-07-01

Alfonso Basin is a small margin basin formed by extensional tectonics in the actively rifting, seismically active Gulf of California. The basin is centered at 24°40' N and 110° 38' W, and is a closed depression (maximum depth 420 m) with an effective sill depth of about 320 m (deepest sill), a width of 20 km and length of 25 km. Basin floor area below a depth of 350 m is about 260 km 2. The climate is arid to semiarid but was wetter during the early (ca. 10,000-7000 Calendar years Before Present [BP]) and middle Holocene (ca. 7000-4000 Cal. Years BP). Basin-wide turbidity currents reach the floor of Alfonso Basin at centennial to millennial intervals. The peninsular drainages tributary to the basin are small and have maximum flood discharges of the order of 10 4m 3. The basin-floor turbidites thicker than 1 cm have volumes of the order of 10 6m 3 to 10 8m 3 and require a much larger source. The largest turbidite seen in our cores is ca. 1 m thick in the central basin floor and was deposited 4900 Calendar Years Before Present (BP). Two smaller major events occurred about 1500 and 2800 Cal. Years BP. Seismicity over the past century of record shows a clustering of larger epicenters along faults forming the eastern Gulf side of Alfonso Basin. In that period there have been four earthquakes with magnitudes above 7.0 but all are distant from the basin. Frequency of such earthquakes in the basin vicinity is probably millennial. It is concluded that the basin-wide turbidites thicker than 1 cm must be generated by slope failures on the eastern side of the basin at roughly millennial intervals. The thin flood turbidites have a peninsular source at centennial frequencies.

Clay minerals behaviour in thin sandy clay-rich lacustrine turbidites (Lake Hazar, Turkey)

Science.gov (United States)

El Ouahabi, Meriam; Hubert-Ferrari, Aurelia; Lamair, Laura; Hage, Sophie

2017-04-01

Turbidites have been extensively studied in many different areas using cores or outcrop, which represent only an integrated snapshot of a dynamic evolving flow. Laboratory experiments provide the missing relationships between the flow characteristics and their deposits. In particular, flume experiments emphasize that the presence of clay plays a key role in turbidity current dynamics. Clay fraction, in small amount, provides cohesive strength to sediment mixtures and can damp turbulence. However, the degree of flocculation is dependent on factors such as the amount and size of clay particles, the surface of clay particles, chemistry and pH conditions in which the clay particles are dispersed. The present study focuses on thin clayey sand turbidites found in Lake Hazar (Turkey) occurring in stacked thin beds. Depositional processes and sources have been previously studied and three types were deciphered, including laminar flows dominated by cohesion, transitional, and turbulence flow regimes (Hage et al., in revision). For the purpose of determine the clay behavior in the three flow regimes, clay mineralogical, geochemical measurements on the cores allow characterising the turbidites. SEM observations provide further information regarding the morphology of clay minerals and other clasts. The study is particularly relevant given the highly alkaline and saline water of the Hazar Lake. Clay minerals in Hazar Lake sediments include kaolinite (1:1-type), illite and chlorite (2:1-type). Hazar lake water is alkaline having pH around 9.3, in such alkaline environment, a cation-exchange reaction takes place. Furthermore, in saline water (16‰), salts can act as a shield and decrease the repulsive forces between clay particle surfaces. So, pH and salt content jointly impact the behaviour of clays differently. Since the Al-faces of clay structures have a negative charge in basic solutions. At high pH, all kaolinite surfaces become negative-charged, and then kaolinite

Techniques used in the exploration of turbidite reservoirs in a frontier setting - Helland Hansen setting, Voering Basin, offshore Mid Norway

Energy Technology Data Exchange (ETDEWEB)

Sanchez-Ferrer, F.; James, S.D.; Lak, B.; Evans, A.M.

1998-12-31

In the 15th Norwegian licensing round there was awarded operation of the Helland Hansen deep water license. Subsurface interpretation commenced towards the end of 1996, following completion of a 1540 km{sup 2} 3-D seismic survey. The main exploration target comprise Turonian to Coniacian turbidite sands within a large fault-bound dip closure. This presentation describes various techniques applied in the exploration of this new turbidite play, with emphasis on the study of the reservoir potential. A methodology of integrated analysis is presented. Through these efforts, a greater understanding of the lithological and depositional models in this non-calibrated area has progressively been achieved. 5 refs., 11 figs.

Processes that initiate turbidity currents and their influence on turbidites: A marine geology perspective

Science.gov (United States)

Piper, David J.W.; Normark, William R.

2009-01-01

How the processes that initiate turbidity currents influence turbidite deposition is poorly understood, and many discussions in the literature rely on concepts that are overly simplistic. Marine geological studies provide information on the initiation and flow path of turbidity currents, including their response to gradient. In case studies of late Quaternary turbidites on the eastern Canadian and western U.S. margins, initiation processes are inferred either from real-time data for historical flows or indirectly from the age and contemporary paleogeography, erosional features, and depositional record. Three major types of initiation process are recognized: transformation of failed sediment, hyperpycnal flow from rivers or ice margins, and resuspension of sediment near the shelf edge by oceanographic processes. Many high-concentration flows result from hyperpycnal supply of hyperconcentrated bedload, or liquefaction failure of coarse-grained sediment, and most tend to deposit in slope conduits and on gradients turbidity flows. In most basins, there is a complex feedback between different types of turbidity-current initiation, the transformation of the flows, and the associated slope morphology. As a result, there is no simple relationship between initiating process and type of deposit.

Influence of pre-tectonic carbonate facies architecture on deformation patterns of syntectonic turbidites, an example from the central Mexican fold-thrust belt

Science.gov (United States)

Vásquez Serrano, Alberto; Tolson, Gustavo; Fitz Diaz, Elisa; Chávez Cabello, Gabriel

2018-04-01

The Mexican fold-thrust belt in central México excellently exposes relatively well preserved syntectonic deposits that overlay rocks with lateral lithostratigraphic changes across the belt. We consider the deformational effects of these changes by investigating the geometry, kinematics and strain distribution within syntectonic turbidites, which are deposited on top of Albian-Cenomanian shallow and deep water carbonate layers. Field observations and detailed structural analysis at different stratigraphic and structural levels of the Late Cretaceous syntectonic formation are compared with the deformation as a function of lithological and structural variations in the underlying carbonate units, to better understand the effect of these lithostratigraphic variations on deformation, kinematics, strain distribution and propagation of deformation. From our kinematic analyses, we conclude that the syntectonic strata are pervasively affected by folding in all areas and that deformation partitioning localized shear zones at the boundaries of this unit, particularly along the contact with massive carbonates. At the boundaries with massive platformal carbonates, the turbidites are strongly deformed by isoclinal folding with a pervasive sub-horizontal axial plane cleavage and 70-60% shortening. In contrast, contacts with thinly-bedded carbonate layers (basinal facies), do not show strain localization, and have horizontal shortening of 50-40% that is accommodated by buckle folds with a less pervasive, steeply dipping cleavage. The mechanical properties variations in the underlying pre-tectonic units as a function of changes in lithostratigraphy fundamentally control the deformation in the overlying syntectonic strata, which is an effect that could be expected to occur in any deformed sedimentary sequence with such variations.

Source of marine turbidites on the Andaman-Nicobar Islands: Nicobar Fan, Bengal Fan or paleo-Irrawaddy?

Science.gov (United States)

Carter, A.

2017-12-01

Marine turbidites from an axially fed submarine fan are intermittently exposed across the entire chain of the Andaman-Nicobar Islands. Known as the Andaman Flysch (AF) and loosely assigned to the Paleogene, it has been proposed that these rocks are sourced from the Himalaya and thus provide a unique window into early stages of orogenesis. Where the turbidites came from has been subject to debate; they are either Bengal Fan or forearc deposits cut off from the Bengal Fan and possibly sourced from the Irrawaddy delta. Following recent IODP drilling in the eastern Indian Ocean (Expeditions 354 and 362) it is now possible resolve this by comparing the provenance of AF turbidites with the Bengal and Nicobar Fans. The Andaman Flysch can be traced as detached outcrops all along the western side of the main islands of Andaman over a strike length of more than 200 km. Exposures along the east coast are confined to South Andaman Island. Petrographic and geochemical data show a common continental crust signal with minor contributions from arc material. But, there are also differences whereby west coast sandstones show significantly higher quartz content and less feldspars and rock fragments. Staurolite is also present in all samples from the western side, but is absent from east coast samples. Both detrital zircon U-Pb and Bulk rock Nd data record the presence of arc material likely from Myanmar. Detrital zircon data from the Nicobar Fan match the Andaman turbidites and indicate sources from the Greater and Tethyan Himalaya mixed with sediment from the Burmese arc. Transfer of Irrawaddy derived sediment to the Nicobar Fan is ruled out as sediment transfer across the fore-arc to the west was restricted by the then exposed Yadana and M8 highs in the north and the Sewell and Alcock Rises to the south. Sediment isopachs of the Martaban back arc basin, the main north-south-oriented depocentre in the Andaman Sea related to the development of the Thanlwin -Irrawaddy delta system

The Late-Quaternary climatic signal recorded in a deep-sea turbiditic levee (Rhône Neofan, Gulf of Lions, NW Mediterranean): palynological constraints

Science.gov (United States)

Beaudouin, Célia; Dennielou, Bernard; Melki, Tarek; Guichard, François; Kallel, Nejib; Berné, Serge; Huchon, Agnès

2004-11-01

Siliciclastic turbidites represent huge volumes of sediments, which are of particular significance for (1) petroleum researchers, interested in their potential as oil reservoirs and (2) sedimentologists, who aim at understanding sediment transport processes from continent to deep-basins. An important challenge when studying marine turbidites has been to establish a reliable chronology for the deposits. Indeed, conventional marine proxies applied to hemipelagic sediments are often unreliable in detrital clays. In siliciclastic turbidites, those proxies can be used only in hemipelagic intervals, providing a poor constraint on their chronology. In this study, we have used sediments from the Rhône Neofan (NW Mediterranean Sea) to demonstrate that pollen grains can provide a high-resolution chronostratigraphical framework for detrital clays in turbidites. Vegetation changes occurring from the end of Marine Isotopic Stage 3 to the end of Marine Isotopic Stage 2 (from ˜30 to ˜18 ka cal. BP) are clearly recorded where other proxies have failed previously, mainly because the scarcity of foraminifers in these sediments prevented any continuous Sea Surface Temperature (SST) record and radiocarbon dating to be obtained. We show also that the use of palynology in turbidite deposits is able to contribute to oceanographical and sedimentological purposes: (1) Pinus pollen grains can document the timing of sea-level rise, (2) the ratio between pollen grains transported from the continent via rivers and dinoflagellate cysts (elutriating) allows us to distinguish clearly detrital sediments from pelagic clays. Finally, taken together, all these tools show evidence that the Rhône River disconnected from the canyon during the sea-level rise and thus evidence the subsequent rapid starvation of the neofan at 18.5 ka cal. BP. Younger sediments are hemipelagic: the frequency of foraminifers allowed to date sediments with radiocarbon. First results of Sea Surface Temperature obtained on

Tectonic control on turbiditic sedimentation: The Late Cretaceous-Eocene successions in the Sinop-Boyabat Basin of north-central Turkey

Energy Technology Data Exchange (ETDEWEB)

Janbu, Nils Erik

2004-07-01

The aim of this study: Tectonics is widely recognized by geologists as the single most important factor controlling the development, filling and deformation of sedimentary basins. In general terms, the role of tectonics seems rather ''obvious'' to most geologists, because we know reasonably well as what tectonics ''can do'' as the agent of structural deformation. Therefore, the role of tectonics is often invoked as a kind of ballpark variable - as the obvious cause of ''subsidence'' or ''uplift'' - and seems to some authors even too obvious to mention. Relatively little attempt has been in sedimentological and stratigraphic studies to recognize as to what effects exactly the tectonic activity had on sedimentation in a particular basin. The principal aim of the present study has been to improve our understanding of how tectonic activity can affect deep-water turbiditic sedimentation in a particular basin, including its ''external'' influences (basin geometry, basin-margin configuration, sediment source/supply and relative sea-level change) and ''internal'' effects (basin-floor subsidence, seafloor deformation). Foreland basins are some of the most active tectonically, and the Sinop- Boyabat Basin is a fascinating case of a rift converted into a foreland basin and increasingly deformed. Summary of papers: The main part of the field study, concerned with the sedimentology and facies analysis of the turbiditic succession, is summarized in Papers 1-3, which put special emphasis on the physical character and morphodynamic evolution of the depositional systems and on the tectonic control on their development. Paper 4 focuses on the frequency distribution of bed thickness data collected by detailed logging of various turbiditic assemblages: siliciclastic deposits of nonchannelized currents (lobe and overbank facies); siliciclastic deposits of poorly confined, aggradational channels; siliciclastic deposits of well-defined sinuous channels nested into channel complexes; and

Asymmetrical cross-current turbidite facies tract in a structurally-confined mini-basin (Priabonian-Rupelian, Ranzano Sandstone, northern Apennines, Italy)

NARCIS (Netherlands)

Tinterri, R.; Laporta, M.; Ogata, K.

2017-01-01

This work discusses the stratigraphy and facies analysis of the Ranzano Sandstone, in the northern Apennines (Italy), a confined low-efficiency turbidite system deposited in a series of small piggy-back basins, which show strong analogies with intraslope minibasins commonly observed in divergent

The Characteristics of Turbidite Beds of Southwest Ryukyu Trench Floor: A new Approach From the X-ray Fluorescence Core Scanning Analysis

Science.gov (United States)

Hsiung, K. H.; Kanamatsu, T.; Ikehara, K.; Usami, K.; Saito, S.; Murayama, M.

2017-12-01

The southwest Ryukyu Trench near Taiwan is an ideal place for source-to-sink studies based on the distinctive sediment transport route between the terrestrial sediment source in Taiwan and the marine sink in the Ryukyu Trench. Using the bathymetric and seismic reflection data, we develop a sediment transport routes for understanding the ultimate sink of the southwest Ryukyu Trench floor. The southwest Ryukyu Trench floor can be regarded as the most distal depositional basin and isolated from the Ryukyu forearc basins. In addition, part of sediment from the proximal sources of the Ryukyu Islands and Yaeyama accretionary prism could be transported to the trench floor. We collected the piston core, PC04, from the southwest Ryukyu Trench floor of 6,147 m water depth in 3.23 m core length from cruise KR15-18, 2015. The coring site locates behind the natural levee of an obvious channel in the Ryukyu trench floor. The PC04 is composed of gray silty clay interbedded with numerous silt layers. Most of the silt layers are less than 2 cm in thickness. Based upon the core observation, X-ray fluorescence core scanning analysis and 14C age determinations, thirty-seven individual and thin beds were determined as turbidites. The results of X-ray fluorescence core scanning analysis provide continuous and high-resolution (1.0 mm of each point) assessment of relative change in the elemental ratios. Ca/Fe is a proxy for the terrigenous component of the sediment, indicating the High Ca and low Fe of each turbidite layers. Zr/Rb ratios of the marine sediments commonly used in the reflection of the original grain size variation. A large part of deep-sea turbidite beds are characterized by high Ca/Fe and Zr/Rb ratio values. These turbidite beds can be linked spatially over a distance of ˜200 km via submarine canyons within the Taiwan orogen. However, it is difficult to be linked temporally to certain events.

Provenance and evolution of miocene turbidite sedimentation in the central Apennines, Italy

Science.gov (United States)

Chiocchini, Ugo; Cipriani, Nicola

1992-05-01

A study of the siliciclastic detritus within the calcareous Miocene turbidite sandstones of the central Apennines has elucidated the provenance of these sandstones. Three ratios: Q/(Q+F), K/F, and Mc/M, have been used and binary correlations of these parameters show that: (1) the sandstones of the Marnoso-Arenacea are characterized by a northern Alpine supply, mainly derived from metamorphic rocks and subordinately from granitic rocks; (2) a secondary supply of western provenance, interbedded within the Marnoso-Arenacea, shows a typical arkosic composition and suggests that granitic rocks of Alpine-type were associated with the Ligurides; (3) the Urbania and Serraspinosa sandstones consist of detritus derived from sources almost identical to those supplying the Marnoso-Arenacea; (4) all the sandstones of the remaining central Apennine basins are characterized by a siliciclastic supply similar to the arkosic one; the rare carbonate fragments can be referred to the Apennine units. The continuity of the Alpine are in the Tyrrhenian area strongly suggests a connection between the western crystalline units and turbidite sedimentation in the basins examined. The crystalline units are associated with a segment of the Alpine chain tectonically linked to the Liguride nappes (Apennine source areas) during the eastwards migration of the Apennines deformation. The crystalline units were gradually eroded during the Burdigalian to Early Pliocene interval when the Laga basin was completely filled. Currently the term "Alpine" is used as synonymous with northern provenance. However, a detailed study carried out over ten years, revealed a western Alpine supply associated with an Apennine source area; we therefore suggest that it is necessary to distinguish a northern Alpine provenance from a western Alpine supply.

Tectonic control on turbiditic sedimentation: The Late Cretaceous-Eocene successions in the Sinop-Boyabat Basin of north-central Turkey

Energy Technology Data Exchange (ETDEWEB)

Janbu, Nils Erik

2004-07-01

The aim of this study: Tectonics is widely recognized by geologists as the single most important factor controlling the development, filling and deformation of sedimentary basins. In general terms, the role of tectonics seems rather ''obvious'' to most geologists, because we know reasonably well as what tectonics ''can do'' as the agent of structural deformation. Therefore, the role of tectonics is often invoked as a kind of ballpark variable - as the obvious cause of ''subsidence'' or ''uplift'' - and seems to some authors even too obvious to mention. Relatively little attempt has been in sedimentological and stratigraphic studies to recognize as to what effects exactly the tectonic activity had on sedimentation in a particular basin. The principal aim of the present study has been to improve our understanding of how tectonic activity can affect deep-water turbiditic sedimentation in a particular basin, including its ''external'' influences (basin geometry, basin-margin configuration, sediment source/supply and relative sea-level change) and ''internal'' effects (basin-floor subsidence, seafloor deformation). Foreland basins are some of the most active tectonically, and the Sinop- Boyabat Basin is a fascinating case of a rift converted into a foreland basin and increasingly deformed. Summary of papers: The main part of the field study, concerned with the sedimentology and facies analysis of the turbiditic succession, is summarized in Papers 1-3, which put special emphasis on the physical character and morphodynamic evolution of the depositional systems and on the tectonic control on their development. Paper 4 focuses on the frequency distribution of bed thickness data collected by detailed logging of various turbiditic assemblages: siliciclastic deposits of nonchannelized currents (lobe and overbank facies); siliciclastic deposits of poorly

From obc seismic to porosity volume: A pre-stack analysis of a turbidite reservoir, deepwater Campos Basin, Brazil

Science.gov (United States)

Martins, Luiz M. R.

The Campos Basin is the best known and most productive of the Brazilian coastal basins. Turbidites are, by far, the main oil-bearing reservoirs. Using a four component (4-C) ocean-bottom-cable (OBC) seismic survey I set out to improve the reservoir characterization in a deep-water turbidite field in the Campos Basin. In order to achieve my goal, pre-stack angle gathers were derived and PP and PS inversion were performed. The inversion was used as an input to predict the petrophysical properties of the reservoir. Converting seismic reflection amplitudes into impedance profiles not only maximizes vertical resolution but also minimizes tuning effects. Mapping the porosity is extremely important in the development of a hydrocarbon reservoirs. Combining seismic attributes derived from the P-P data and porosity logs I use linear multi-regression and neural network geostatistical tools to predict porosity between the seismic attributes and porosity logs at the well locations. After predicting porosity in well locations, those relationships were applied to the seismic attributes to generate a 3-D porosity volume. The predicted porosity volume highlighted the best reservoir facies in the reservoir. The integration of elastic impedance, shear impedance and porosity improved the reservoir characterization.

3D stratigraphic modeling of the Congo turbidite system since 210 ka: an investigation of factors controlling sedimentation

Science.gov (United States)

Laurent, Dimitri; Picot, Marie; Marsset, Tania; Droz, Laurence; Rabineau, Marina; Granjeon, Didier; Molliex, Stéphane

2017-04-01

The geometry and internal functioning of turbidite systems are relatively well-constrained today. However, the respective role of autogenic (topographic compensation, dynamics of turbidity currents…) and allogenic factors (tectonics, sea-level, climate) governing their architectural evolution is still under debate. The geometry of the Quaternary Congo Fan is characterized by successive sedimentary prograding/retrograding cycles bounded by upfan avulsions, reflecting a periodic control of sedimentation (Picot et al., 2016). Multi-proxy studies revealed a strong interplay between autogenic control and climate forcing as evidenced by changes in fluvial sediment supplies consistent with arid and humid periods in the Congo River Basin. In the light of these results, the aim of this study is to investigate the relative impact of internal and external forcing factors controlling, both in time and space, the formation and evolution of depocenters of the Congo Deep-Sea Fan since 210 ka. This work represents the first attempt to model in 3D the stratigraphic architecture of the Congo turbidite system using DionisosFlow (IFP-EN), a diffusion process-based software. It allows the simulation of sediment transport and the 3D geometry reproduction of sedimentary units based on physical processes such as sea level changes, tectonics, sediment supply and transport. According to the modeling results, the role of topographic compensation in the deep-sea fan geometry is secondary compared to climate changes in the drainage basin. It appears that a periodic variation of sediment discharge and water flow is necessary to simulate the timing and volume of prograding/retrograding sedimentary cycles and more particularly the upfan avulsion events. The best-fit simulations show that the overriding factor for such changes corresponds to the expansion of the vegetation cover in the catchment basin associated to the Milankovitch cycle of precession which controlled the West African Monsoon

Stratigraphic Stacking of Deepmarine Channel Levee Turbidites: Scales of Cyclicity and their Origin. Examples from the Laingsburg Fm. (Karoo, South Africa) and the Rosario Fm. (Baja, Mexico)

Science.gov (United States)

Kane, I. A.; Hodgson, D.

2009-12-01

Thinning upwards of the turbidite beds that form deepmarine channel levees is a common motif reported from modern and recent levees on the seafloor, from subsurface examples, and from outcropping ancient examples. Because levees are thought to be built by deposition from turbidity currents superelevated over their channel form, the volume and style of overbank deposition are controlled primarily by the relationship between levee height (i.e., thalweg to crest) and flow thickness, determining the amount of overspill. Thus stratigraphic variability of turbidite thickness is explained by some change in either or both of those factors, which may arise autocyclicly or allocyclicly. Variation in the ratio of intra-channel and extra-channel deposition can be an autocyclic stratigraphic response, e.g., in bypass dominated systems, thalweg aggradation may be retarded with respect to levee aggradation, hence as levee relief increases, flows become more confined and, given a relatively narrow range of flow sizes, the volume of overbank flow and deposit thickness decrease with stratigraphic height. However, the same stratigraphic response of the levee may occur due to allocyclic flow magnitude variation, i.e., through decreasing flow magnitude. In both the autocyclic and allocyclic case the stratigraphic response of the levee may be one of thinning upwards, even if the overall system response may be one of progradation (autocyclic bypassing case) or retrogradation (allocyclic decreasing flow magnitude case), with entirely different connotations for sequence stratigraphic interpretation. Here we report examples of different scales of bed thickness cyclicity (both thickening and thinning upward cycles superimposed by smaller scale cycles) within levees of the Rosario Formation, Baja California, Mexico, and from the Laingsburg Formation, Karoo, South Africa, and, together with published examples, discuss criteria for the recognition, and drivers of, autocyclic and allocyclic bed

Distal turbidite fan/lobe succession of the Late Oligocene Zuberec Fm. - architecture and hierarchy (Central Western Carpathians, Orava-Podhale basin)

Science.gov (United States)

Starek, Dušan; Fuksi, Tomáš

2017-08-01

A part of the Upper Oligocene sand-rich turbidite systems of the Central Carpathian Basin is represented by the Zuberec Formation. Sand/mud-mixed deposits of this formation are well exposed in the northern part of the basin, allowing us to interpret the turbidite succession as terminal lobe deposits of a submarine fan. This interpretation is based on the discrimination of three facies associations that are comparable to different components of distributive lobe deposits in deep-water fan systems. They correspond to the lobe off-axis, lobe fringe and lobe distal fringe depositional subenvironments, respectively. The inferences about the depositional paleoenvironment based on sedimentological observations are verified by statistical analyses. The bed-thickness frequency distributions and vertical organization of the facies associations show cyclic trends at different hierarchical levels that enable us to reconstruct architectural elements of a turbidite fan. First, small-scale trends correspond with shift in the lobe element centroid between successive elements. Differences in the distribution and frequency of sandstone bed thicknesses as well as differences in the shape of bed-thickness frequency distributions between individual facies associations reflect a gradual fining and thinning in a down-dip direction. Second, meso-scale trends are identified within lobes and they generally correspond to the significant periodicity identified by the time series analysis of the bed thicknesses. The meso-scale trends demonstrate shifts in the position of the lobe centroid within the lobe system. Both types of trends have a character of a compensational stacking pattern and could be linked to autogenic processes. Third, a largescale trend documented by generally thickening-upward stacking pattern of beds, accompanied by a general increase of the sandstones/mudstones ratio and by a gradual change of percentage of individual facies, could be comparable to lobe-system scale. This

Mineralogy of Nicobar Fan turbidites (IODP Leg 362): Himalayan provenance and diagenetic control.

Science.gov (United States)

Limonta, M.; Garzanti, E.; Ando, S.; Carter, A.; Milliken, K. L.; Pickering, K. T.

2017-12-01

In this study we use quantitative petrographic and heavy-mineral data on silt-sized and sand-sized sediments from the Nicobar Fan turbiditic depositional system to unravel their provenance and discriminate between pre-depositional and post-depositional processes controlling sediment mineralogy. Eighteen samples from the two drill sites U1480 e U1481, collected down to a depth of 1400 m during International Ocean Discovery Expedition 362, were selected for analysis. A complete section of the sedimentary section overlying oceanic basaltic basement was recovered at the U1480 drill site, whereas the U1481 drill site, located 35 km to the southeast, focused on the deeper interval of the sedimentary section overlying oceanic basement. Here we illustrate the compositional trends observed throughout the recovered succession, and compare heavy-mineral suites characterizing sediments drilled at the two U1480 and U1481 sites to check for potential differences in sediment provenance over a relatively short distance in trench settings. Diagenetic control with increasing burial depth was also specifically investigated. In Pleistocene sediments at depths of a few tens of meters only, rich heavy-mineral assemblages include mainly hornblende, epidote, and garnet, associated with apatite, clinopyroxene, tourmaline, sillimanite, kyanite, zircon, titanite, and rare staurolite and rutile, testifying to long-distance provenance from the Himalayan range via the Ganga-Brahmaputra fluvio-deltaic-turbiditic system. Heavy-mineral concentration shows a progressive decrease with burial depth, pointing to selective diagenetic dissolution of less durable detrital minerals. Clinopyroxene becomes rare below 400 m depth and was not recorded below 500 m depth, where amphibole decreases notably in relative abundance. More durable heavy minerals, including zircon, tourmaline, apatite, garnet and epidote, consequently tend to be relatively enriched with increasing age and burial depth. Petrographic and

Heavy mineral sorting and distributions within massive sandstone divisions (Bouma A divisions) of Brushy Canyon Formation turbidites

Science.gov (United States)

Motanated, K.; Tice, M. M.

2009-12-01

KANNIPA MOTANATED and MICHAEL M. TICE Department of Geology and Geophysics, Texas A&M University, College Station, TX 77843-3115, USA Sediment sorting data are commonly used for interpreting depositional environments, analyzing mechanisms of deposition and transportation, and inferring relative transport distance of sediments. Typically, sorting in sandstones is estimated by point-counting thin sections which is a time consuming procedure and requires cutting sections of rock samples. We demonstrate a new technique for quantifying sediment sorting using element distribution maps obtained by x-ray fluorescence microscopy. We show that hydraulic sorting of Zr- and Ti- bearing grains (probably zircon and rutile, respectively) results in characteristic vertical profiles of Zr and Ti abundances within the Bouma A divisions of turbidites of the Brushy Canyon Formation, Delaware Basin, southern New Mexico. Zr- and Ti- bearing grains decrease in abundance and diameter from bases to tops of A divisions in every sample examined in this study. These results contrast with previous observations which suggest that grading in Brushy Canyon Formation structureless sandstones is absent or rare. The data support turbiditic interpretations of these rocks against traction current interpretations which rely on the lack of textural grading. Grading is reflected in vertical profiles of Ti/Al, Zr/Al and Zr/Ti ratios, which each decrease upward. These compositional variations could potentially be used as geochemical proxies for physical sorting, and might be useful for inferring depositional processes and relative transport distances.

Compositional variations and differential diagenesis in Miocene turbidites from the western coast of Mallorca (Balearic Islands, Spain)

Science.gov (United States)

Felder, Sonja; Westphal, Hildegard; Munnecke, Axel; Mateu Vicens, Guillem

2010-05-01

Compositional variations and differential diagenesis in Miocene turbidites from the western coast of Mallorca (Balearic Islands, Spain) Sonja Felder (1), Hildegard Westphal (1), Axel Munnecke (2), Guillem Mateu Vicens (1,3) (1) MARUM and Department of Geosciences, Universität Bremen, Leobener Straße, 28359 Bremen, Germany (2) GeoZentrum Nordbayern, Universität Erlangen-Nürnberg, Loewenichstr. 28, 91054 Erlangen, Germany (3) Dipartimento di Scienze della Terra, Università di Roma "La Sapienza", Ple Aldo 7 Moro, 5. I-00185 Roma, Italy Cyclic alternations of limestone and marl beds crop out along the western coast of the Island of Mallorca. This Miocene succession is traditionally interpreted to represent more weathering-resistant turbidites interlayered by softer hemipelagic background sediment. However, the cementation patterns that dominate the appearance of the outcrop do not always consistently follow sedimentary layering; locally the cemented beds are systematically oblique to the sedimentary layers. Compositional studies demonstrate that differences in non-carbonate fraction, carbonate concentration and fossil content (e.g. foraminiferal assemblages) trace sedimentary bedding, regardless the diagenetic style. Limestone versus marl lithology, in contrast, is defined by the diagenetic style, tight cementation by calcite cements in the limestones versus low porosity and compaction in the marls. The reason for this striking pattern of diagenetic bedding cross-cutting sedimentary layers is assumed to be related to tectonic fracturing, opening pathways for diagenetic fluids. This example cautions the straight-forward interpretation of limestone-marl alternations as direct witnesses of environmental or climatic variations.

The radioisotopically constrained Viséan onset of turbidites in the Moravian-Silesian part of the Rhenohercynian foreland basin (Central European Variscides)

Science.gov (United States)

Jirásek, Jakub; Otava, Jiří; Matýsek, Dalibor; Sivek, Martin; Schmitz, Mark D.

2018-03-01

The Březina Formation represents the initiation of siliciclastic flysch turbidite sedimentation at the eastern margin of Bohemian Massif or within the Rhenohercynian foreland basin. Its deposition started after drowning of the Devonian carbonate platform during Viséan (Mississippian) times, resulting in a significant interval of black siliceous shale and variegated fossiliferous shale deposition in a starved basin. Near the top of the Březina Formation an acidic volcanoclastic layer (tuff) of rhyolitic composition has been dated with high precision U-Pb zircon chemical abrasion isotope dilution method at 337.73 ± 0.16 Ma. This new radiometric age correlates with the previously inferred stratigraphic age of the locality and the current calibration of the Early Carboniferous geologic time scale. Shales of the Březina Formation pass gradually upwards into the siliciclastics of the Rozstání Formation of the Drahany culm facies. Thus our new age offers one of the few available radioisotopic constraints on the time of onset of siliciclastic flysch turbidites in the Rhenohercynian foreland basin of the European Variscides.

Distal turbidite fan/lobe succession of the Late Oligocene Zuberec Fm. – architecture and hierarchy (Central Western Carpathians, Orava–Podhale basin

Directory of Open Access Journals (Sweden)

Starek Dušan

2017-08-01

Full Text Available A part of the Upper Oligocene sand-rich turbidite systems of the Central Carpathian Basin is represented by the Zuberec Formation. Sand/mud-mixed deposits of this formation are well exposed in the northern part of the basin, allowing us to interpret the turbidite succession as terminal lobe deposits of a submarine fan. This interpretation is based on the discrimination of three facies associations that are comparable to different components of distributive lobe deposits in deep-water fan systems. They correspond to the lobe off-axis, lobe fringe and lobe distal fringe depositional subenvironments, respectively. The inferences about the depositional paleoenvironment based on sedimentological observations are verified by statistical analyses. The bed-thickness frequency distributions and vertical organization of the facies associations show cyclic trends at different hierarchical levels that enable us to reconstruct architectural elements of a turbidite fan. First, small-scale trends correspond with shift in the lobe element centroid between successive elements. Differences in the distribution and frequency of sandstone bed thicknesses as well as differences in the shape of bed-thickness frequency distributions between individual facies associations reflect a gradual fining and thinning in a down-dip direction. Second, meso-scale trends are identified within lobes and they generally correspond to the significant periodicity identified by the time series analysis of the bed thicknesses. The meso-scale trends demonstrate shifts in the position of the lobe centroid within the lobe system. Both types of trends have a character of a compensational stacking pattern and could be linked to autogenic processes. Third, a largescale trend documented by generally thickening-upward stacking pattern of beds, accompanied by a general increase of the sandstones/mudstones ratio and by a gradual change of percentage of individual facies, could be comparable to lobe

Sequence stratigraphy of Taciba and Rio Bonito formations in Mafra, SC area, eastern Parana Basin, Brazil; Estratigrafia de sequencias das formacoes Taciba e Rio Bonito (Membro Triunfo) na regiao de Mafra/SC, leste da Bacia do Parana

Energy Technology Data Exchange (ETDEWEB)

NONE

2005-05-01

The Taciba and Rio Bonito ('lower' Triunfo Mbr) formations are divided into six depositional sequences based on cores, gamma-ray and electrical logs from shallow drillings from northern Santa Catarina State, Brazil. Each sequence is formed by two systems tracts, a lower one, sandy (low stand) and an upper one, shaly (high stand). The Taciba Formation has three sequences, S{sub 0} to S{sub 2}; sequence S{sub 0} has a thick turbidite sandstone at the base (Rio Segredo Member) that pinches out towards the eastern margin and even disappears in the Mafra outcrop area. Sequence S{sub 1} varies from a thin fluvial-estuarine system to a thick turbidite sandstone of a channelled fan system; S{sub 1} upper shaly system tract is marine in well PP-11, and it is glacially influenced in well PP-10. Sequence S{sub 2} is a thick sandstone body of shallow marine origin, but restricted to one well (PP-11); its upper shaly tract is dominated by massive siltstones intercalated with thin, distal tempestites. The 'lower' Triunfo Member (or 'Taciba- Triunfo transition') begins with the arrival of deltaic clastics of sequence S{sub 3} lower tract, coarsening-up from medial- to proximal delta front sandstones. Sequence S{sub 4} is quite similar to S{sub 3}, both showing sandstone pro gradation from north to south, as opposed to the southwest-sourced transgressive diamictites. Sequence S{sub 5} consists of fluvial deposits at well PP-12, and two transgressive cycles from wells PP-11 to PP-9, each one of them composed of fluvial-estuarine to marine systems. Well PP-10 is an exception, where the lower cycle presents de glaciation to marine deposits. (author)

Summary of November 2010 meeting to evaluate turbidite data for constraining the recurrence parameters of great Cascadia earthquakes for the update of national seismic hazard maps

Science.gov (United States)

Frankel, Arthur D.

2011-01-01

This report summarizes a meeting of geologists, marine sedimentologists, geophysicists, and seismologists that was held on November 18–19, 2010 at Oregon State University in Corvallis, Oregon. The overall goal of the meeting was to evaluate observations of turbidite deposits to provide constraints on the recurrence time and rupture extent of great Cascadia subduction zone (CSZ) earthquakes for the next update of the U.S. national seismic hazard maps (NSHM). The meeting was convened at Oregon State University because this is the major center for collecting and evaluating turbidite evidence of great Cascadia earthquakes by Chris Goldfinger and his colleagues. We especially wanted the participants to see some of the numerous deep sea cores this group has collected that contain the turbidite deposits. Great earthquakes on the CSZ pose a major tsunami, ground-shaking, and ground-failure hazard to the Pacific Northwest. Figure 1 shows a map of the Pacific Northwest with a model for the rupture zone of a moment magnitude Mw 9.0 earthquake on the CSZ and the ground shaking intensity (in ShakeMap format) expected from such an earthquake, based on empirical ground-motion prediction equations. The damaging effects of such an earthquake would occur over a wide swath of the Pacific Northwest and an accompanying tsunami would likely cause devastation along the Pacifc Northwest coast and possibly cause damage and loss of life in other areas of the Pacific. A magnitude 8 earthquake on the CSZ would cause damaging ground shaking and ground failure over a substantial area and could also generate a destructive tsunami. The recent tragic occurrence of the 2011 Mw 9.0 Tohoku-Oki, Japan, earthquake highlights the importance of having accurate estimates of the recurrence times and magnitudes of great earthquakes on subduction zones. For the U.S. national seismic hazard maps, estimating the hazard from the Cascadia subduction zone has been based on coastal paleoseismic evidence of great

Geometry of the proximal part of the modern turbidite depositional system of the Carapebus Formation, Campos Basin: a model for reservoir heterogeneities; Geometria da porcao proximal do sistema deposicional turbiditico moderno da Formacao Carapebus, Bacia de Campos; modelo para heterogeneidades de reservatorio

Energy Technology Data Exchange (ETDEWEB)

Machado, Luis Claudio Ribeiro; Kowsmann, Renato Oscar; Almeida Junior, Waldemar de; Murakami, Celso Yoshihito; Schreiner, Simone; Miller, Dennis James; Piauilino, Pedro Orlando Vasconcelos [PETROBRAS, Rio de Janeiro, RJ (Brazil). Exploracao e Producao. Unidade de Servico Submarino]. E-mail: machadolc@petrobras.com.br

2004-11-01

The deep-water marine sedimentary environment of the Cenozoic of the Campos Basin is examined at the modern sea floor, where it can be better understood. This environment is responsible for the genesis of the turbidite systems of the Carapebus Formation, the reservoirs that hold more than 90% of Brazil's petroleum reserves. The study was developed with the records of regional side-scan sonar, swath bathymetry, sub-bottom profiler data, standard multichannel 3D seismic surveys and piston cores covering almost the entire basin. After leaving the Almirante Camara Canyon, the turbiditic flows erode the muddy debris apron surrounding the continental slope and begin to deposit thick layers of clean sand into a big trough in water depths of 1800 m to 3000 m. The trough is 3.5 km wide, 150 m deep, 150 km long, and is formed by a chain of salt withdrawal mini-basins. In some places the sea floor is flat enough to develop today a depositional lobe, in all aspects analogous to the best, geologically ancient petroleum reservoirs in the basin. Aspects of the system: 1) the arcosean sands are brought by the river, cross the shelf, the incised valley, the canyon, and deposit as turbidites - they do not originate from a collapse of the continental slope; 2) a wide muddy debris apron surrounds the continental slope (slope apron), and represents a huge volume of sediment in the Campos Basin ; 3) the turbidites do not develop a submarine fan, but are deposited in an elongated trough formed by salt tectonics; 4) the turbidite beds, both in the lobe or in the trough, are not deposited during a single episode, but in multiple events over significant geologic time in which small channels which brought the turbidites avulse and meander along the entire depositional area, building a single amalgamated bed; 5) classic channel-levees are not present because this system comprises a sandy braid plain and the levees are as sandy as the channel; 6) a hierarchical depositional model for bulb

Convolute laminations and load structures in turbidites as indicators of flow reflections and decelerations against bounding slopes. Examples from the Marnoso-arenacea Formation (northern Italy) and Annot Sandstones (south eastern France)

Science.gov (United States)

Tinterri, R.; Muzzi Magalhaes, P.; Tagliaferri, A.; Cunha, R. S.

2016-10-01

This work discusses the significance of particular types of soft-sediment deformations very common within turbidite deposits, namely convolute laminations and load structures. Detailed facies analyses of the foredeep turbidites in the Marnoso-arenacea Formation (northern Italy) and Annot Sandstones (south eastern France) show that these deformational structures tend to increase near morphological obstacles, concomitantly with contained-reflected beds. The lateral and vertical distribution of convolute laminae and load structures, as well as their geometry, has a well-defined depositional logic related to flow decelerations and reflections against bounding slopes. This evidence suggests an interaction between fine-grained sediment and the presence of morphologic relief, and impulsive and cyclic-wave loadings, which are produced by flow impacts or reflected bores and internal waves related to impinging bipartite turbidity currents.

The coupling of dynamics and permeability in the hydrocarbon accumulation period controls the oil-bearing potential of low permeability reservoirs: a case study of the low permeability turbidite reservoirs in the middle part of the third member of Shahejie Formation in Dongying Sag

DEFF Research Database (Denmark)

Yang, Tian; Cao, Ying-Chang; Wang, Yan-Zhong

2016-01-01

The relationships between permeability and dynamics in hydrocarbon accumulation determine oilbearing potential (the potential oil charge) of low permeability reservoirs. The evolution of porosity and permeability of low permeability turbidite reservoirs of the middle part of the third member...... facies A and diagenetic facies B do not develop accumulation conditions with low accumulation dynamics in the late accumulation period for very low permeability. At more than 3000 m burial depth, a larger proportion of turbidite reservoirs are oil charged due to the proximity to the source rock. Also...

Revista de Investigacion Educativa (Journal of Educational Research).

Science.gov (United States)

Revista de Investigacion Educativa, 1997

1997-01-01

The two issues of this journal include the following articles (Titles are translated into English): "General Panorama of Research on Intercultural Education in Europe" (Margarita Bartolome Pina); "Incidence of Some Educational, Social, and Affective Factors in Alcohol Consumption by Teenagers" (Elvira Repetto Talavera, Ma.…

Facies-related fracturing in turbidites: insights from the Marnoso-Arenacea Fm. (Northern Apennines, Italy)

Science.gov (United States)

Ogata, Kei; Storti, Fabrizio; Balsamo, Fabrizio; Bedogni, Enrico; Tinterri, Roberto; Fetter, Marcos; Gomes, Leonardo; Hatushika, Raphael

2016-04-01

Natural fractures deeply influence subsurface fluid flow, exerting a primary control on resources like aquifers, hydrocarbons and geothermal reservoirs, and on environmental issues like CO2 storage and nuclear waste disposal. In layered sedimentary rocks, depositional processes-imprinted rock rheology favours the development of both mechanical anisotropy and heterogeneity on a wide range of scales, and are thus expected to strongly influence location and frequency of fractures. To better constrain the contribution of stratigraphic, sedimentological and petrophysical attributes, we performed a high-resolution, multidisciplinary study on a selected stratigraphic interval of jointed foredeep turbidites in the Miocene Marnoso-arenacea Formation (Northern Apennines, Italy), which are characterised by a great lateral and vertical variability of grain-size and depositional structures. Statistical relationships among field and laboratory data significantly improve when the single facies scale is considered, and, for similar facies recording different evolutionary stages of the parent turbidity currents, we observed a direct correlation between the three-dimensional anisotropies of rock hardness tensors and the normalized fracture frequencies, testifying for the primary sedimentary flow-related control on fracture distributions.

Soft-sediment deformations (convolute lamination and load structures) in turbidites as indicators of flow reflections against bounding slopes

Science.gov (United States)

Tinterri, Roberto; Muzzi Magalhaes, Pierre; Tagliaferri, Alessio; Cunha, Rogerio S.; Laporta, Michele

2015-04-01

Soft-sediment deformations, such as convolute laminations, load structures and water escapes are very rapid deformations that occur in unconsolidated sediments near the depositional surface during or shortly after deposition and before significant diagenesis. These types of deformations develop when primary stratifications are deformed by a system of driving forces, while the sediment is temporarily in a weakened state due to the action of a deformation mechanism know as liquidization. This deformation occurs if the applied stress exceeds the sediment strength, either through an increase in the applied stress or through a temporary reduction in sediment strength. Liquidization mechanisms can be triggered by several agents, such as seismic shaking, rapid sedimentation with high-fallout rates or cyclic-pressure variations associated with storm waves or breaking waves. Consequently, soft-sediment deformations can be produced by different processes and form ubiquitous sedimentary structures characterizing many sedimentary environments. However, even though these types of structures are relatively well-known in terms of geometry and sedimentary characteristics, many doubts arise when the understanding of deformation and trigger mechanisms is attempted. As stressed also by the recent literature, the main problem lies in the fact that the existing approaches for the identification of triggering agents rely on criteria that are not diagnostic or not applicable to outcrop-based studies, because they are not always based on detailed facies analysis related to a paleoenvironmental-context approach. For this reason, this work discusses the significance of particular types of soft-sediment deformations that are very common in turbidite deposits, namely convolute laminations and load structures, especially on the basis of a deep knowledge of the stratigraphic framework and geological setting in which these structures are inserted. More precisely, detailed facies analyses of the

Selective transport of palynomorphs in marine turbiditic deposits: An example from the Ascension-Monterey Canyon system offshore central California

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McGann, Mary

2017-01-01

The pollen assemblage of a deep-sea core (15G) collected at lower bathyal depths (3491 m) on a levee of Monterey Canyon off central California was investigated to gain insights into the delivery processes of terrigenous material to submarine fans and the effect this transport has on the palynological record. Thirty-two samples were obtained down the length of the core, 19 from hemipelagic and mixed mud deposits considered to be the background record, and 13 others from displaced flow deposits. The pollen record obtained from the background samples documents variations in the terrestrial flora as it adapted to changing climatic conditions over the last 19,000 cal yrs BP. A Q-mode cluster analysis defined three pollen zones: a Glacial Pollen Zone (ca. 20,000–17,000 cal yr BP), an overlying Transitional Pollen Zone (ca. 17,000–11,500 cal yr BP), and an Interglacial Pollen Zone (ca. 11,500 cal yr BP to present). Another Q-mode cluster analysis, of both the background mud and flow deposits, also defined these three pollen zones, but four of the 13 turbiditic deposits were assigned to pollen zones older than expected by their stratigraphic position. This was due to these samples containing statistically significant fewer palynomorphs than the background muds as well as being enriched (∼10–35% in some cases) in hydraulically-efficient Pinus pollen. A selective bias in the pollen assemblage, such as demonstrated here, may result in incorrect interpretations (e.g., climatic shifts or environmental perturbations) based on the floral record, indicating turbiditic deposits should be avoided in marine palynological studies. Particularly in the case of fine-grained flow deposits that may not be visually distinct, granulometry and grain size frequency distribution curves may not be enough to identify these biased deposits. Determining the relative abundance and source of displaced shallow-water benthic foraminifera entrained in these sediments serves as an excellent

Upper Pleistocene turbidite sand beds and chaotic silt beds in the channelized, distal, outer-fan lobes of the Mississippi fan

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Nelson, C.H.; Twichell, D.C.; Schwab, W.C.; Lee, H.J.; Kenyon, Neil H.

1992-01-01

Cores from a Mississippi outer-fan depositional lobe demonstrate that sublobes at the distal edge contain a complex local network of channelized-turbidite beds of graded sand and debris-flow beds of chaotic silt. Off-lobe basin plains lack siliciclastic coarse-grained beds. The basin-plain mud facies exhibit low acoustic backscatter on SeaMARC IA sidescan sonar images, whereas high acoustic backscatter characteristic of the lobe sand and silt facies. The depth of the first sand-silt layer correlates with relative backscatter intensity and stratigraphic age of the distal sublobes (i.e., shallowest sand = highest backscatter and youngest sublobe). The high proportion (>50%) of chaotic silt compared to graded sand in the distal, outer-fan sublobes may be related to the unstable, muddy, canyon-wall source areas of the extensive Mississippi delta-fed basin slope. A predominace of chaotic silt in cores or outcrops from outer-fan lobes thus may predict similar settings for ancient fans.

onshore, niger delta

African Journals Online (AJOL)

User

2016-12-02

Dec 2, 2016 ... A reservoir is a subsurface rock that has .... sequence (potential source rock), turbidite sand. (potential ... diapirs, roll-over anticlines, collapsed growth fault crests ..... Lehner P., De Ruiter, P.A.C., (1977):Structural History.

Journal of Earth System Science | Indian Academy of Sciences

Indian Academy of Sciences (India)

: white massive tuff with ill-defined bedding contacts (facies-A) and; dominantly green tuff exhibiting well-developed turbidite sequence with up-section change from a massive unit to plane laminated units to ripple drift lamination (facies-B).

Felsic tuff from Rutland Island – A pyroclastic flow deposit in ...

Indian Academy of Sciences (India)

: • white massive tuff with ill-defined bedding contacts (facies-A) and. • dominantly green tuff exhibiting well-developed turbidite sequence with up-section change from a massive unit to plane laminated units to ripple drift lamination (facies-B).

Feasibility of Optimizing Recovery and Reserves from a Mature and Geological Complex Multiple Turbidite Offshore Calif. Reservoir through the Drilling and Completion of a Trilateral Horizontal Well, Class III

Energy Technology Data Exchange (ETDEWEB)

Pacific Operators Offshore, Inc.

2001-04-04

The intent of this project was to increase production and extend the economic life of this mature field through the application of advanced reservoir characterization and drilling technology, demonstrating the efficacy of these technologies to other small operators of aging fields. Two study periods were proposed; the first to include data assimilation and reservoir characterization and the second to drill the demonstration well. The initial study period showed that a single tri-lateral well would not be economically efficient in redevelopment of Carpinteria's multiple deep water turbidite sand reservoirs, and the study was amended to include the drilling of a series of horizontal redrills from existing surplus well bores on Pacific Operators' Platform Hogan.

Die muttekopfgosau (Lechtaler Alpen, Tirol/Österreich): Sedimentologie und Beckenentwicklung

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Ortner, H.

1994-03-01

In the Eastern Alps compression during orogeny in the Upper Cretaceous caused crustal thickening, isostatic uplift and gravitational adjustment of the unstable orogenic wedge. This process triggered extensional basin formation on the back of the orogen (Gosau Basins). The basin fill of the Muttekopf Gosau Basin is arranged in megacycles, the first one comprising alluvial fan sediments and “Inoceramus marls” of the Lower Gosau Complex (Faupl et al. 1987) of Santonian age. Three other cycles follow (Upper Gosau Complex, Campanian to Maastrichtian), consisting of turbiditic fining upward sequences, that are indicative for extensional tectonics during basin formation, as subsidence events prevent formation of autocyclic coarsening upward sequences and therefore prograding of the turbidite system. Deposition of the 1st and 2nd Megacycle occured below the CCD (Carbonate Compensation Depth). The carbonate rich 3rd Megacycle was deposited probably below the CCD after a period of palaeogeographic reorganisation (uplift?) in the source area.

The structure of the window of Bobbio : (northern Apennines, Italy)

NARCIS (Netherlands)

den Haan, J.A.

1979-01-01

Field work in the tectonic window of Bobbio has demonstrated the following tectonic units: Tuscan unit, the lowermost unit in the window. It is composed of a turbiditic sequence of Oligocene or Early Miocene age, folded into a large recumbent syncline with a gently NE-dipping NE limb and a steeply

The structure of the window of Bobbio : (northern Apennines, Italy)

NARCIS (Netherlands)

Haan, J.A. den

1979-01-01

Field work in the tectonic window of Bobbio has demonstrated the following tectonic units: Tuscan unit, the lowermost unit in the window. It is composed of a turbiditic sequence of Oligocene or Early Miocene age, folded into a large recumbent syncline with a gently NE-dipping NE limb and a

Sedimentary facies control on mechanical and fracture stratigraphy in turbidites

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Ogata, Kei; Storti, Fabrizio; Balsamo, Fabrizio; Tinterri, Roberto; Bedogni, Enrico; Fetter, Marcos; Gomes, Leonardo; Hatushika, Raphael

2017-01-01

Natural fracture networks exert a first-order control on the exploitation of resources such as aquifers, hydrocarbons, and geothermal reservoirs, and on environmental issues like underground gas storage and waste disposal. Fractures and the mechanical stratigraphy of layered sequences have been

Giant landslides and turbidity currents in the Agadir Canyon Region, NW-Africa

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Krastel, Sebastian; Wynn, Russell B.; Stevenson, Christopher; Feldens, Peter; Mehringer, Lisa; Schürer, Anke

2017-04-01

Coring and drilling of the Moroccan Turbidite System off NW-Africa revealed a long sequence of turbidites, mostly sourced from the Moroccan continental margin and the volcanic Canary Islands. The largest individual flow deposits in the Moroccan Turbidite System contain sediment volumes >100 km3, although these large-scale events are relatively infrequent with a recurrence interval of 10,000 years (over the last 200,000 years). The largest siliciclastic flow in the last 200,000 years was the 'Bed 5 event', which transported 160 km3 of sediment up to 2000 km from the Agadir Canyon region to the southwest Madeira Abyssal Plain. While the Moroccan Turbidite System is extremely well investigated, almost no data from the source region, i.e. the Agadir Canyon, are available. Understanding why some submarine landslides remain as coherent blocks of sediment throughout their passage downslope, while others mix and disintegrate almost immediately after initial failure, is a major scientific challenge, which was addressed in the Agadir Canyon source region during RV Maria S. Merian Cruise MSM32 in late 2013. A major landslide area was identified 200 km south of the Agadir Canyon. A landslide was traced from this failure area to the Agadir Canyon. This landslide entered the canyon in about 2500 m water depth. Despite a significant increase in slope angle, the landslide did not disintegrate into a turbidity current when entering the canyon but moved on as landslide for at least another 200 km down the canyon. The age of the landslide ( 145 ka) does not correspond to any major turbidte deposit in the Moroccan Turbidite System, further supporting the fact that the landslide did not disintegrate into a major turbidity current. A core taken about 350 m above the thalweg in the head region of Agadir Canyon shows a single coarse-grained turbidite, which resembles the composition of the Bed 5 event in the Madeira Abyssal Plain. Hence, the Bed 5 turbidite originated as a failure in the

Detrital zircon provenance from three turbidite depocenters of the Middle-Upper Triassic Songpan-Ganzi complex, central China: Record of collisional tectonics, erosional exhumation, and sediment production

Science.gov (United States)

Weislogel, A.L.; Graham, S.A.; Chang, E.Z.; Wooden, J.L.; Gehrels, G.E.

2010-01-01

To test the idea that the voluminous upper Middle to Upper Triassic turbidite strata in the Songpan-Ganzi complex of central China archive a detrital record of Dabie ultrahigh-pressure (UHP) terrane unroofing, we report 2080 single detrital U-Pb zircon ages by sensitive high-resolution ion microprobe-reverse geometry (SHRIMP-RG) and laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) analysis from 29 eastern Songpan-Ganzi complex sandstone samples. Low (Th/U zircons, consistent with crystallization under UHP conditions, are rare in eastern Songpan-Ganzi complex zircon, and U-Pb ages of low Th/U zircons are incompatible with a Dabie terrane source. An unweighted pair group method with arithmetic mean nearest-neighbor analysis of Kolmogorov-Smirnov two-sample test results reveals that the eastern Songpan-Ganzi complex is not a single contiguous turbidite system but is instead composed of three subsidiary depocenters, each associated with distinct sediment sources. The northeastern depocenter contains zircon ages characterized by Paleozoic and bimodally distributed Precambrian zircon populations, which, together with south-to southeast-directed paleocurrent data, indicate derivation from the retro-side of the Qinling-Dabie (Q-D) collisional orogen wedge. In the central depocenter, the dominantly Paleozoic detrital zircon signature and south-to southwest-oriented paleocurrent indicators reflect a profusion of Paleozoic zircon grains. These data are interpreted to reflect an influx of material derived from erosion of Paleozoic supra-UHP rocks of the Dabie terrane in the eastern Qinling-Dabie orogen, which we speculate may have been enhanced by development of a monsoonal climate. This suggests that erosional unroofing played a significant role in the initial phase of UHP exhumation and likely influenced the petrotectonic and structural evolution of the Qinling-Dabie orogen, as evidenced by compressed Triassic isotherms/grads reported in the Huwan

Sediment gravity flows triggered by remotely generated earthquake waves

Science.gov (United States)

Johnson, H. Paul; Gomberg, Joan S.; Hautala, Susan L.; Salmi, Marie S.

2017-06-01

Recent great earthquakes and tsunamis around the world have heightened awareness of the inevitability of similar events occurring within the Cascadia Subduction Zone of the Pacific Northwest. We analyzed seafloor temperature, pressure, and seismic signals, and video stills of sediment-enveloped instruments recorded during the 2011-2015 Cascadia Initiative experiment, and seafloor morphology. Our results led us to suggest that thick accretionary prism sediments amplified and extended seismic wave durations from the 11 April 2012 Mw8.6 Indian Ocean earthquake, located more than 13,500 km away. These waves triggered a sequence of small slope failures on the Cascadia margin that led to sediment gravity flows culminating in turbidity currents. Previous studies have related the triggering of sediment-laden gravity flows and turbidite deposition to local earthquakes, but this is the first study in which the originating seismic event is extremely distant (> 10,000 km). The possibility of remotely triggered slope failures that generate sediment-laden gravity flows should be considered in inferences of recurrence intervals of past great Cascadia earthquakes from turbidite sequences. Future similar studies may provide new understanding of submarine slope failures and turbidity currents and the hazards they pose to seafloor infrastructure and tsunami generation in regions both with and without local earthquakes.

Preliminary analysis of the sandstone accumulation situation at Sha-3 of the Paleogene Series Shakhetsze in the Khekou basin of the Tsziyan region

Energy Technology Data Exchange (ETDEWEB)

Chen, S

1984-01-01

The Khekou basin of the second order which is located in the Eastern part of the Tsziyan basin in the oil and gas Bokhayvan'skiy pool has an area of about 900 km/sup 2/. The main productive level occurs in sandstone beds in the Sha-3 subseries (reaching thickness of about 400 m) of the Shakhetsze series. The Bonan oil field was discovered in this region in 1975. The initially productive deposits were viewed as fluvial-delta; however, studies of recent years, including investigation of the sedimentation sequences and the structures that mark the surfaces of the microscopic level in the core sample, together with an analysis of borehole geophysical data, indicated that the sandy bodies of the productive beds in the basin must be viewed as deposits of turbidite flows and deposits of gravitational flows in channels. Insofar as distribution of the turbidite sandstones differs significantly from the delta, this led to a review of the long-term trends in the neighboring fields.

TRANSITION FROM CARBONATE PLATFORM TO PELAGIC DEPOSITION (MID JURASSIC- LATE CRETACEOUS, VOURINOS MASSIF, NORTHERN GREECE

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NICOLAOS CARRAS

2004-03-01

Full Text Available A Jurassic- Cretaceous carbonate succession crops out along the Zyghosti Rema, Kozani (Northern Greece. The substratum consists of the ophiolitic succession of the Vourinos Massif (Pelagonian Domain: serpentinites tectonically overlain by basalts, with thin lenses of radiolarian cherts of middle Bathonian age. The contact with the overlying Jurassic limestones is tectonic. Eight informal units have been distinguished within the Mesozoic limestones, from the base upwards. (A bioclastic, intraclastic and oolitic packstone (Callovian- Oxfordian. (B bioclastic packstone and coral boundstone (Oxfordian . (C bioclastic and oncoidal wackestone with Clypeina jurassica (Oxfordian- Upper Kimmeridgian. (D (Upper Kimmeridgian- Portlandian: oncoidal packstone and rudstone (facies D1; intraclastic and bioclastic grainstone and packstone (facies D2; neptunian dykes with intraclastic and bioclastic wackestone and packstone filling (facies D3; neptunian dykes with Fe-Mn rich laterite filling and with pink silty filling of early Late Cretaceous age. An unconformity surface, due to emersion and erosion of the platform during the latest Jurassic- Early Cretaceous, is overlain by (E intraclastic, bioclastic packstone and grainstone (Cenomanian. (F massive body of debrites with coral, echinoderm, algae and rudist large clasts (facies F1 (Cenomanian; turbiditic beds of bioclastic, intraclastic and lithoclastic rudstone and grainstone (facies F2. (G thin bedded bioclastic mudstone and wackestone with planktonic foraminifers and radiolarians, alternating with turbiditic beds of bioclastic, intraclastic packstone and rudstone and with conglomeratic levels and slumped beds of the previous turbidites (upper Santonian- lower Campanian. (H: bioclastic packstone with planktonic foraminifers (facies H1 (lower Campanian - ?Maastrichtian; amalgamated turbiditic beds of bioclastic wackestone and packstone with planktonic foraminifers (facies H2; turbiditic beds of bioclastic

Equatorial origin for Lower Jurassic radiolarian chert in the Franciscan Complex, San Rafael Mountains, southern California

Science.gov (United States)

Hagstrum, J.T.; Murchey, B.L.; Bogar, R.S.

1996-01-01

Lower Jurassic radiolarian chert sampled at two localities in the San Rafael Mountains of southern California (???20 km north of Santa Barbara) contains four components of remanent magnetization. Components A, B???, and B are inferred to represent uplift, Miocene volcanism, and subduction/accretion overprint magnetizations, respectively. The fourth component (C), isolated between 580?? and 680??C, shows a magnetic polarity stratigraphy and is interpreted as a primary magnetization acquired by the chert during, or soon after, deposition. Both sequences are late Pliensbachian to middle Toarcian in age, and an average paleolatitude calculated from all tilt-corrected C components is 1?? ?? 3?? north or south. This result is consistent with deposition of the cherts beneath the equatorial zone of high biologic productivity and is similar to initial paleolatitudes determined for chert blocks in northern California and Mexico. This result supports our model in which deep-water Franciscan-type cherts were deposited on the Farallon plate as it moved eastward beneath the equatorial productivity high, were accreted to the continental margin at low paleolatitudes, and were subsequently distributed northward by strike-slip faulting associated with movements of the Kula, Farallon, and Pacific plates. Upper Cretaceous turbidites of the Cachuma Formation were sampled at Agua Caliente Canyon to determine a constraining paleolatitude for accretion of the Jurassic chert sequences. These apparently unaltered rocks, however, were found to be completely overprinted by the A component of magnetization. Similar in situ directions and demagnetization behaviors observed in samples of other Upper Cretaceous turbidite sequences in southern and Baja California imply that these rocks might also give unreliable results.

Searching for the seafloor signature of the 21 May 2003 Boumerdès earthquake offshore central Algeria

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A. Cattaneo

2012-07-01

Full Text Available Shaking by moderate to large earthquakes in the Mediterranean Sea has proved in the past to potentially trigger catastrophic sediment collapse and flow. On 21 May 2003, a magnitude 6.8 earthquake located near Boumerdès (central Algerian coast triggered large turbidity currents responsible for 29 submarine cable breaks at the foot of the continental slope over ~150 km from west to east. Seafloor bathymetry and backscatter imagery show the potential imprints of the 2003 event and of previous events. Large slope scarps resulting from active deformation may locally enhance sediment instabilities, although faults are not directly visible at the seafloor. Erosion is evident at the foot of the margin and along the paths of the numerous canyons and valleys. Cable breaks are located at the outlets of submarine valleys and in areas of turbiditic levee overspilling and demonstrate the multi-source and multi-path character of the 2003 turbiditic event. Rough estimates of turbidity flow velocity are not straightforward because of the multiple breaks along the same cable, but seem compatible with those measured in other submarine cable break studies elsewhere.

While the signature of the turbidity currents is mostly erosional on the continental slope, turbidite beds alternating with hemipelagites accumulate in the distal reaches of sediment dispersal systems. In perspective, more chronological work on distal turbidite successions offshore Algeria offers promising perspectives for paleoseismology reconstructions based on turbidite dating, if synchronous turbidites along independent sedimentary dispersal systems are found to support triggering by major earthquakes. Preliminary results on sediment core PSM-KS23 off Boumerdès typically show a 800-yr interval between turbidites during the Holocene, in accordance with the estimated mean seismic cycle on land, even if at this stage it is not yet possible to prove the earthquake origin of all the turbidites.

Flood, Seismic or Volcanic Deposits? New Insights from X-Ray Computed Tomography

Science.gov (United States)

Van Daele, M. E.; Moernaut, J.; Vermassen, F.; Llurba, M.; Praet, N.; Strupler, M. M.; Anselmetti, F.; Cnudde, V.; Haeussler, P. J.; Pino, M.; Urrutia, R.; De Batist, M. A. O.

2014-12-01

Event deposits, such as e.g. turbidites incorporated in marine or lacustrine sediment sequences, may be caused by a wide range of possible triggering processes: failure of underwater slopes - either spontaneous or in response to earthquake shaking, hyperpycnal flows and floods, volcanic processes, etc. Determining the exact triggering process remains, however, a major challenge. Especially when studying the event deposits on sediment cores, which typically have diameters of only a few cm, only a small spatial window is available to analyze diagnostic textural and facies characteristics. We have performed X-ray CT scans on sediment cores from Chilean, Alaskan and Swiss lakes. Even when using relatively low-resolution CT scans (0.6 mm voxel size), many sedimentary structures and fabrics that are not visible by eye, are revealed. For example, the CT scans allow to distinguish tephra layers that are deposited by fall-out, from those that reached the basin by river transport or mud flows and from tephra layers that have been reworked and re-deposited by turbidity currents. The 3D data generated by the CT scans also allow to examine relative orientations of sedimentary structures (e.g. convolute lamination) and fabrics (e.g. imbricated mud clasts), which can be used to reconstruct flow directions. Such relative flow directions allow to determine whether a deposit (e.g. a turbidite) had one or several source areas, the latter being typical for seismically triggered turbidites. When the sediment core can be oriented (e.g. using geomagnetic properties), absolute flow directions can be reconstructed. X-ray CT scanning, at different resolution, is thus becoming an increasingly important tool for discriminating the exact origin of EDs, as it can help determining whether e.g. an ash layer was deposited as fall out from an ash cloud or fluvially washed into the lake, or whether a turbidite was triggered by an earthquake or a flood.

Stratigraphy and stable isotope geochemistry of the carbonate sequence from the Paraguay belt

International Nuclear Information System (INIS)

Santos, Roberto Ventura.; Alvarenga, Carlos Jose Souza de; Dantas, Elton Luiz

2001-01-01

Two main Neoproterozoic carbonate sequences occur central Brazil both of which are stratiphicaly above glacial derived sediments. An older carbonate sequence occurs over the Sao Francisco Craton and in the surrounding folded belts (Rio Preto, Aracuai Ribeira and Brasilia). These carbonates overlie glacial diamictites that were related to the 'Sturtian' event dated between 0.7 and 0.9 Ga (Toulkeridis et al. 1999, Santos et al., 2000). A second carbonate sequence is described in the Paraguay Belt and postdated Vendian/Varegian glaciation sediments from the end of the Neoproterozoic. This glacial event has been reported in many studies concerning the Gondwana and the Laurentia supercontinent (Trompette, 1996; Condon and Prave, 2000; Myrow and Kaufman, 1999). In the Paraguay Belt the Vendian- Varangian glaciation rocks are characterized by a glaciomarine sequence, that occur at the border of the basin, and by glacial derived turbidites deposits, that occur in the deeper parts of the basin (Alvarenga and Trompette, 1992). Near the city of Corumba this glaciomarine sequence is overlaid by carbonate rocks containing Ediacaran-like fauna in which has been described Corumbella werneri and Cloudina Lucianoi (Hahn et al., 1982; Walde et al., 1982; Zaine and Fairchild, 1985; 1987). These carbonates have been interpreted as cap carbonates and the age of their fossils have been attributed to the Vendian Superior (590-545 MA) (Alvarenga and Trompette, 1992, Trompette 1996). Isotope stratigraphy studies have been widely used to study cap carbonate rocks that overlie Sturtian and Vendian- Varagian glaciogenic rocks. Stratigraphic correlation of these units is usually difficult because their lack fossils and there is no precise dating method that could be applied to these rocks. Hence, most studies concerning Neoproterozoic carbonates have concentrated on their stromatilites and microfossils content as well as on carbon isotope variations. In the present study, we present new carbon

Universal sequence map (USM of arbitrary discrete sequences

Directory of Open Access Journals (Sweden)

Almeida Jonas S

2002-02-01

Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

Tectonic and Sedimentation Interactions in the East Caribbean Subduction Zone: AN Overview from the Orinoco Delta to the Barbados Accretionary Prism

Science.gov (United States)

Deville, E.

2011-12-01

Recent marine geophysical acquisitions and piston-coring allow to better understand the close interactions between the sand-rich Orinoco turbidite system and the compressional structures of the Barbados prism. Because of the morphologic and tectonic control in the east-Caribbean active margin, the Orinoco turbiditic pattern system does not exhibit a classic fan geometry. The sea-floor geometry between the slope of the front of the Barbados prism and the slope of the South-American margin induces the convergence of the turbidite channels toward the abyssal plain, at the front of the accretionary prism. Also, whereas in most passive margins the turbidite systems are organized upstream to downstream as canyon, then channel-levee, then lobes, here, due to the tectonic control, the sedimentary system is organized as channel-levee, then canyons, then channelized lobes. At the edge of the Orinoco platform, the system has multiple sources with several distributaries and downward the channel courses are complex with frequent convergences or divergences that are emphasized by the effects of the undulating seafloor tectonic morphologies associated with active thrust tectonics and mud volcanism. On top of the accretionary prism, turbidite sediments are filling transported piggy-back basins whose timing of sedimentation vs. deformation is complex. Erosion processes are almost absent on the highly subsiding Orinoco platform and in the upper part of the turbidite system. Erosion processes develop mostly between 2000 and 4000 m of water depth, above the compressional structures of the Barbados prism (canyons up to 3 km wide and 300 m deep). In the abyssal plain, turbiditic channels develop on very long distance (> 1000 km) joining the mid-Atlantic channel (sourced mostly by the Amazon), filling several elongated basins corresponding to transform faults (notably the Barracuda Basin), and finally sourcing the Puerto-Rico trench, the deepest morphologic depression of this region

Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

Science.gov (United States)

Deroost, Natacha; Coomans, Daphné

2018-02-01

We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

The geology and geochemistry of Madeira abyssal plain sediments: a review

International Nuclear Information System (INIS)

Weaver, P.P.E.; Thomson, J.; Jarvis, I.

1989-01-01

The Madeira Abyssal Plain was chosen by the Nuclear Energy Agency (NEA) as a study area for high-level radioactive waste disposal in 1980. Subsequently, the area has been intensively investigated, in particular by the Geological Survey of the Netherlands, the Institute of Oceanographic Sciences, and latterly by the international ESOPE expedition organized by the NEA Seabed Working Group. The large data set from this area of 2 0 x 2 0 includes 16,000 km of low-frequency seismic lines, 28,000 km of high-frequency seismic lines, 70,000 km 2 of GLORIA sidescan and 120 sediment cores. Core coverage extends through the upper 34 m of the sediment column, representing the last 730,000 years, and shows deposition dominated by turbidite sedimentation. Seismic profiles indicate that total thickness of turbidites averages 350 m with about 200 m of pelagic sediment beneath. Thus the turbidites continue considerably deeper than proposed penetrator emplacement depths of 30-70 m. Individual turbidites are separated by thin pelagic layers which can be dated and show the turbidites to be emplaced at the beginning and end of glacial periods. (author)

Quantum-Sequencing: Fast electronic single DNA molecule sequencing

Science.gov (United States)

Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

2014-03-01

A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

Multimodal sequence learning.

Science.gov (United States)

Kemény, Ferenc; Meier, Beat

2016-02-01

While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

Deposits of Large-scale Mass Movements in the Sediments of Hallstätter See (Austria) - Recurrent Natural Hazards at a UNESCO World Cultural Heritage Site

Science.gov (United States)

Lauterbach, S.; Strasser, M.; Tjallingii, R.; Kowarik, K.; Reschreiter, H.; Spatl, C.; Brauer, A.

2017-12-01

The cultural importance of underground salt mining in Hallstatt (Austria), which is documented since the Middle Bronze Age, has been recognized already 20 years ago by assigning the status of a UNESCO World Cultural Heritage Site to the Hallstatt area, particularly because of the wealth of archaeological artefacts from the Early Iron Age. Local mining activity is well documented for prehistoric times and known to have been repeatedly affected by large-scale mass movements, for example at the end of the Bronze Age and during the Late Iron Age. In contrast, evidence of mining activity between the 5th and late 13th century AD is scarce, which could be related to socio-economic changes but also to continued mass movement activity, possibly biasing the archaeological record. Within the present study, a 15.63-m-long 14C-dated sediment core from Hallstätter See has been investigated with respect to the deposits of large-scale mass movements. Most of the lake sediment sequence consists of cm- to sub-mm-scale laminated carbonate mud with frequently intercalated small-scale turbidites, reflecting seasonally variable detrital input from the tributaries, but two major event layers clearly stand out. The upper one comprises a 2.45-m-thick basal mass transport deposit (containing folded laminated sediments, homogenized sediments with liquefaction structures, and coarse gravel) and an overlying 1.45-m-thick co-genetic turbidite. From the lower event layer only the topmost part of the turbiditic sequence with a (minimum) thickness of 1.49 m was recovered. Based on their sedimentological characteristics, both event layers are interpreted as the subaqueous continuation of large-scale mass movements, which occurred at ca. 1050 and 2300 cal. years BP and possibly originated from the rock walls along the western lake shore where also the salt mining area is located. This indicates that mass movement activity not only threatened prehistoric salt mining, but occurred also repeatedly

Diagenesis and reservoir quality evolution of palaeocene deep-water, marine sandstones, the Shetland-Faroes Basin, British continental shelf

Energy Technology Data Exchange (ETDEWEB)

Mansurbeg, H. [Department of Earth Sciences, Uppsala University, Villavaegen 16, SE 752 36 Uppsala (Sweden); Morad, S. [Department of Earth Sciences, Uppsala University, Villavaegen 16, SE 752 36 Uppsala (Sweden); Department of Petroleum Geosciences, The Petroleum Institute, P.O. Box 2533, Abu Dhabi (United Arab Emirates); Salem, A. [Faculty of Education at Kafr El-Sheikh, Tanta University, Kafr El-Sheikh (Egypt); Marfil, R.; Caja, M.A. [Departmento Petrologia y Geoquimica, Facultad de Geologia, UCM, 28040 Madrid (Spain); El-ghali, M.A.K. (Geology Department, Al-Fateh University, P.O. Box 13696, Libya); Nystuen, J.P. [Department of Geosciences, University of Oslo, P.O. Box 1047 Blindern, NO-0316 Oslo (Norway); Amorosi, A. [Department of Earth Sciences, University of Bologna, Via Zamboni 67, 40127 Bologna (Italy); Garcia, D. [Centre SPIN, Department GENERIC, Ecole Nationale Superieure des Mines de Saint Etienne 158, Cours Fauriel 42023, Saint-Etienne (France); La Iglesia, A. [Instituto de Geologia Economica (CSIC-UCM), Facultad de Geologia, UCM, 28040 Madrid (Spain)

2008-06-15

The Palaeocene, deep-water marine sandstones recovered from six wells in the Shetland-Faroes Basin represent lowstand, transgressive and highstand systems tract turbiditic sediments. Mineralogic, petrographic, and geochemical analyses of these siliciclastics are used to decipher and discuss the diagenetic alterations and subsequent reservoir quality evolution. The Middle-Upper Palaeocene sandstones (subarkoses to arkoses) from the Shetland-Faroes Basin, British continental shelf are submarine turbiditic deposits that are cemented predominantly by carbonates, quartz and clay minerals. Carbonate cements (intergranular and grain replacive calcite, siderite, ferroan dolomite and ankerite) are of eogenetic and mesogenetic origins. The eogenetic alterations have been mediated by marine, meteoric and mixed marine/meteoric porewaters and resulted mainly in the precipitation of calcite ({delta}{sup 18}O{sub V-PDB}=-10.9 permille and -3.8 permille), trace amounts of non-ferroan dolomite, siderite ({delta}{sup 18}O{sub V-PDB}=-14.4 permille to -0.6 permille), as well as smectite and kaolinite in the lowstand systems tract (LST) and highstand systems tract (HST) turbiditic sandstone below the sequence boundary. Minor eogenetic siderite has precipitated between expanded and kaolinitized micas, primarily biotite. The mesogenetic alterations are interpreted to have been mediated by evolved marine porewaters and resulted in the precipitation of calcite ({delta}{sup 18}O{sub V-PDB}=-12.9 permille to -7.8 permille) and Fe-dolomite/ankerite ({delta}{sup 18}O{sub V-PDB}=-12.1 permille to -6.3 permille) at temperatures of 50-140 and 60-140 C, respectively. Quartz overgrowths and outgrowth, which post- and pre-date the mesogenetic carbonate cements is more common in the LST and TST of distal turbiditic sandstone. Discrete quartz cement, which is closely associated with illite and chlorite, is the final diagenetic phase. The clay minerals include intergranular and grain replacive

Novel expressed sequence tag- simple sequence repeats (EST ...

African Journals Online (AJOL)

Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

Genome Sequence Databases (Overview): Sequencing and Assembly

Energy Technology Data Exchange (ETDEWEB)

Lapidus, Alla L.

2009-01-01

From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

Energy Technology Data Exchange (ETDEWEB)

Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

2007-02-21

Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

Integrating sequence stratigraphy and rock-physics to interpret seismic amplitudes and predict reservoir quality

Science.gov (United States)

Dutta, Tanima

This dissertation focuses on the link between seismic amplitudes and reservoir properties. Prediction of reservoir properties, such as sorting, sand/shale ratio, and cement-volume from seismic amplitudes improves by integrating knowledge from multiple disciplines. The key contribution of this dissertation is to improve the prediction of reservoir properties by integrating sequence stratigraphy and rock physics. Sequence stratigraphy has been successfully used for qualitative interpretation of seismic amplitudes to predict reservoir properties. Rock physics modeling allows quantitative interpretation of seismic amplitudes. However, often there is uncertainty about selecting geologically appropriate rock physics model and its input parameters, away from the wells. In the present dissertation, we exploit the predictive power of sequence stratigraphy to extract the spatial trends of sedimentological parameters that control seismic amplitudes. These spatial trends of sedimentological parameters can serve as valuable constraints in rock physics modeling, especially away from the wells. Consequently, rock physics modeling, integrated with the trends from sequence stratigraphy, become useful for interpreting observed seismic amplitudes away from the wells in terms of underlying sedimentological parameters. We illustrate this methodology using a comprehensive dataset from channelized turbidite systems, deposited in minibasin settings in the offshore Equatorial Guinea, West Africa. First, we present a practical recipe for using closed-form expressions of effective medium models to predict seismic velocities in unconsolidated sandstones. We use an effective medium model that combines perfectly rough and smooth grains (the extended Walton model), and use that model to derive coordination number, porosity, and pressure relations for P and S wave velocities from experimental data. Our recipe provides reasonable fits to other experimental and borehole data, and specifically

Blind sequence-length estimation of low-SNR cyclostationary sequences

CSIR Research Space (South Africa)

Vlok, JD

2014-06-01

Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

Directory of Open Access Journals (Sweden)

Kirkness Ewen

2006-10-01

Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

Small scale turbidity currents in a tectonically active submarine graben, the Gulf of Corinth (Greece): their significance in dispersing mine tailings and their relevance to basin filling

Science.gov (United States)

Papatheodorou, G.; Stefatos, A.; Christodoulou, D.; Ferentinos, G.

2003-04-01

The Gulf of Corinth is an intra-plate active graben within the Aegean microplate, which is characterized by high frequency occurrence of gravitative mass movements. A detailed marine survey in Antikyra bay, on the northern margin of the graben, was carried out (i) to study the bathymetry and morphology of the seafloor and (ii) to examine the distribution and dispersion of bauxite “red-mud” tailings and the formation of present-day fine grained, thin bedded turbidites. The examination of high resolution seismic profiles has shown that the northern flank of the gulf of Corinth consists of the shelf, slope and basin floor. The shelf has an average width of 10 km and dips very gently at a gradient less than 1.2o to a depth of 300m. The slope extends from the 300m to the 700m isobath with a gradient ranging from 5o to 7.5o. The basin floor deeper than the 700m isobath is flat with a gradient less than 0.1o. The shelf break and upper slope are affected by mass-movements. The seafloor on slope is incised by numerous channels trending in a NNE-SSW direction. The floor of the plain is covered by ponded turbidites. The analysis of cores based on (i) the texture and the structure of the individual layers of the surficial sedimentary cover and (ii) the tracing of bauxite red-mud tailing which have been discharged since 1970 on the upper shelf of the Antikyra Bay, have shown that: (i) Shelf and upper slope sediments are transported to the basin floor by turbidity flows. (ii) The slope surface is affected by the erosional action of the turbidity currents. (iii) The basin floor is covered by thin-bedded fine-grained turbidites whose thickness ranges from 0.8-4 cm. (iv) The individual turbidite beds, which consist of silt and clay, are structureless and are separated by sharp, planar or erosional contacts. (v) Hemipelagic intercalations are absent. The number of turbiditic events recorded in the surveyed area is from 2-5 events over a period of 15 years or 122 to 333 events

Sequence assembly

DEFF Research Database (Denmark)

Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

2009-01-01

Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

Science.gov (United States)

Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

2011-01-01

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

Shotgun protein sequencing.

Energy Technology Data Exchange (ETDEWEB)

Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

2009-06-01

A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

Foundations of Sequence-to-Sequence Modeling for Time Series

OpenAIRE

Kuznetsov, Vitaly; Mariet, Zelda

2018-01-01

The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

Detection of M-Sequences from Spike Sequence in Neuronal Networks

Directory of Open Access Journals (Sweden)

Yoshi Nishitani

2012-01-01

Full Text Available In circuit theory, it is well known that a linear feedback shift register (LFSR circuit generates pseudorandom bit sequences (PRBS, including an M-sequence with the maximum period of length. In this study, we tried to detect M-sequences known as a pseudorandom sequence generated by the LFSR circuit from time series patterns of stimulated action potentials. Stimulated action potentials were recorded from dissociated cultures of hippocampal neurons grown on a multielectrode array. We could find several M-sequences from a 3-stage LFSR circuit (M3. These results show the possibility of assembling LFSR circuits or its equivalent ones in a neuronal network. However, since the M3 pattern was composed of only four spike intervals, the possibility of an accidental detection was not zero. Then, we detected M-sequences from random spike sequences which were not generated from an LFSR circuit and compare the result with the number of M-sequences from the originally observed raster data. As a result, a significant difference was confirmed: a greater number of “0–1” reversed the 3-stage M-sequences occurred than would have accidentally be detected. This result suggests that some LFSR equivalent circuits are assembled in neuronal networks.

Genome Sequencing

DEFF Research Database (Denmark)

Sato, Shusei; Andersen, Stig Uggerhøj

2014-01-01

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

[Complete genome sequencing and sequence analysis of BCG Tice].

Science.gov (United States)

Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

2012-10-04

The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

Lower Tertiary Sedimentary Turbidite Facies at the Chicontepec Basin, East-Central Mexico

Directory of Open Access Journals (Sweden)

Santillán-Piña N.

2011-07-01

Full Text Available The study area comprises the northwestern portion of the Chicontepec Basin at southeastern San Luis Potosí and northeastern Hidalgo States. At the stratigraphy sequences of the Chicontepec Formation from Lower Paleocene in isolated outocrops, were herein interpreted two major sedimentary sub-environments into the fan model: the middle and the external sedimentary settings; the applied criteria for their identification were: (a lithostratigraphic (thickness, geometry and distribution; (b internal and external primary sedimentary structures, and (c intra-formational deformation structures. The sedimentary facies are composed of siliciclastic and calcareous particles sourced from the Sierra Madre Oriental, western; the Tuxpan paleo-island, eastern; and from the Teziutlan Massif, southern; the sediments were massively transported by slideing, slumping, flow debris and turbidity currents, then deposited as massive, tabular, lenticular and lobely in shape at the slope foot and on the sea marine floor.

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

Science.gov (United States)

de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

2000-01-01

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

Directory of Open Access Journals (Sweden)

Jian eWu

2012-11-01

Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

International Nuclear Information System (INIS)

Rauzy, Antoine B.

2011-01-01

A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform

Directory of Open Access Journals (Sweden)

Shan Wei

2018-05-01

Full Text Available Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

Directory of Open Access Journals (Sweden)

Joern Toedling

Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

Depositional environment and sedimentary of the basinal sediments in the Eibiswalder Bucht (Radl Formation and Lower Eibiswald Beds), Miocene Western Styrian Basin, Austria

Science.gov (United States)

Stingl, K.

1994-12-01

The Eibiswald Bucht is a small subbasin of the Western Styrian Basin exposing sediments of Lower Miocene age. In the past the entire sequence exposed in the Eibiswalder Bucht has been interpreted as being of fluvial/lacustrine origin; here, results are presented of detailed sedimentological investigations that lead to a revision of this concept. The lowermost siliciclastic sedimentary unit of the Eibiswalder Bucht sequence is the Radl Formation. It is overlain by the Eibiswald Beds, which are subdivided into the Lower, Middle and Upper Eibiswald Beds. The Radl Formation and the Lower Eibiswald Beds are interpreted as a fan delta complex deposited along NNW-SSE striking faults. Based on the sedimentary facies this fan delta can be subdivided into a subaerial alluvial fan facies group, a proximal delta facies group and a distal delta/prodelta facies group. The Radl Formation comprises the alluvial fan and proximal delta facies groups, the Lower Eibiswald Beds the distal delta/prodelta facies group. The alluvial fan and the proximal delta consist of diverse deposits of gravelly flows. The distal delta/prodelta consists of wave-reworked, bioturbated, low density turbidites intercalated with minor gravelly mass flows. The prodelta can be regarded as as the basin facies of the small and shallow Eibiswalder Bucht, where marine conditions prevailed. The basin was probably in part connected with the Eastern Styrian Basin, the contemporary depositional environment of the Styrian Schlier (mainly turbiditic marine offshore sediments in the Eastern Styrian Basin). Analysis of the clast composition, in conjunction with the paleotransport direction of the coarse delta mass flows of the Radl Formation, shows that the source rocks were exclusively crystalline rocks ranging from greenschists to eclogites.

Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

DEFF Research Database (Denmark)

Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

2012-01-01

Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...

Roles of repetitive sequences

Energy Technology Data Exchange (ETDEWEB)

Bell, G.I.

1991-12-31

The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

Probabilistic Motor Sequence Yields Greater Offline and Less Online Learning than Fixed Sequence.

Science.gov (United States)

Du, Yue; Prashad, Shikha; Schoenbrun, Ilana; Clark, Jane E

2016-01-01

It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session). To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT) task with either a fixed or probabilistic sequence and with or without preliminary knowledge (PK) of the presence of a sequence. The sequence and PK were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge (NPK)) or declarative (fixed sequence; with PK) memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a 2 min break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that PK facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT), we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively). It was found that the two groups who performed the fixed sequence, regardless of PK, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of PK, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence offline. These results suggest that in the SRT task, the fast acquisition of a motor sequence is driven

Nonparametric combinatorial sequence models.

Science.gov (United States)

Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

2011-11-01

This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

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Wang, Ji; Ke, Yue Hua; Zhang, Yong; Huang, Ke Qiang; Wang, Lei; Shen, Xin Xin; Dong, Xiao Ping; Xu, Wen Bo; Ma, Xue Jun

2017-10-01

Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Welded slump-graded sand couplets: evidence for slide generated turbidity currents

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Stanley, Daniel Jean

1982-09-01

Some massive channelized strata preserved in the rock record are characterized by a lower slump member which evolves upward to a turbidite. This merging is indicative of probable generation of sediment gravity flows from submarine sliding. Conditions essential for deposition of such sequences are short transport distance between point of failure and depositional site, and an environment likely to retain both facies. Fan valleys are a likely setting for welded couplets: flowing sand, initiated by the sliding event, comes to rest at nearly the same time and position as the slump mass deposited near the base of the valley wall and in the axis proper.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities

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Baldwin Stephen A

2011-03-01

Full Text Available Abstract Background Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. Results The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. Conclusions PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities.

Science.gov (United States)

Troshin, Peter V; Postis, Vincent Lg; Ashworth, Denise; Baldwin, Stephen A; McPherson, Michael J; Barton, Geoffrey J

2011-03-07

Facilities that provide a service for DNA sequencing typically support large numbers of users and experiment types. The cost of services is often reduced by the use of liquid handling robots but the efficiency of such facilities is hampered because the software for such robots does not usually integrate well with the systems that run the sequencing machines. Accordingly, there is a need for software systems capable of integrating different robotic systems and managing sample information for DNA sequencing services. In this paper, we describe an extension to the Protein Information Management System (PIMS) that is designed for DNA sequencing facilities. The new version of PIMS has a user-friendly web interface and integrates all aspects of the sequencing process, including sample submission, handling and tracking, together with capture and management of the data. The PIMS sequencing extension has been in production since July 2009 at the University of Leeds DNA Sequencing Facility. It has completely replaced manual data handling and simplified the tasks of data management and user communication. Samples from 45 groups have been processed with an average throughput of 10000 samples per month. The current version of the PIMS sequencing extension works with Applied Biosystems 3130XL 96-well plate sequencer and MWG 4204 or Aviso Theonyx liquid handling robots, but is readily adaptable for use with other combinations of robots. PIMS has been extended to provide a user-friendly and integrated data management solution for DNA sequencing facilities that is accessed through a normal web browser and allows simultaneous access by multiple users as well as facility managers. The system integrates sequencing and liquid handling robots, manages the data flow, and provides remote access to the sequencing results. The software is freely available, for academic users, from http://www.pims-lims.org/.

Sequence embedding for fast construction of guide trees for multiple sequence alignment

LENUS (Irish Health Repository)

Blackshields, Gordon

2010-05-14

Abstract Background The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N 2 for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments. Results In this paper, we have tested variations on a class of embedding methods that have been designed for clustering large numbers of complex objects where the individual distance calculations are expensive. These methods involve embedding the sequences in a space where the similarities within a set of sequences can be closely approximated without having to compute all pair-wise distances. Conclusions We show how this approach greatly reduces computation time and memory requirements for clustering large numbers of sequences and demonstrate the quality of the clusterings by benchmarking them as guide trees for multiple alignment. Source code is available for download from http:\\/\\/www.clustal.org\\/mbed.tgz.

Sequencing of BAC pools by different next generation sequencing platforms and strategies

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Scholz Uwe

2011-10-01

Full Text Available Abstract Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.

Long sequence correlation coprocessor

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Gage, Douglas W.

1994-09-01

A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

Next-Generation Sequencing Platforms

Science.gov (United States)

Mardis, Elaine R.

2013-06-01

Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

Optimization of sequence alignment for simple sequence repeat regions

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Ogbonnaya Francis C

2011-07-01

Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

Adaptive Processing for Sequence Alignment

KAUST Repository

Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

2012-01-01

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.

Adaptive Processing for Sequence Alignment

KAUST Repository

Zidan, Mohammed A.

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.

Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

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Marta Brozynska

Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

Science.gov (United States)

Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

2017-07-01

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

Ash turbidites from Southern Italy help understanding the parent eruptions and contributing to geodynamic evolution cadre of the Tyrrhenian sea

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Doronzo, Domenico Maria

2010-05-01

Tephra layers intercalated in sedimentary successions are very interesting since they represent some instants of geodynamic evolution in a sedimentation basin. Furthermore, they can constitute deposits of explosive eruptions whose distal behaviour can be useful for studying the volcanoes activity, especially when pyroclastic deposits in proximal areas are absent. In the Craco area (Matera, Italy), thick ash turbidites intercalated in marine clays deposits have been recently recognized, which interest is related to the considerable cropping out thickness (1 to 5 m), freshness of the material and absence of sedimentary component. Petrography, sedimentology and chemistry of the deposits have been characterized with the aim of defining genesis and deposition of the material. The deposits are essentially made up of ashy pyroclasts, dominated by fresh acidic to intermediate glass, mostly in the form of shards, pumice fragments and groundmass fragments with vitrophyric texture. Rare crystals include Pl, Opx, Cpx, Hbl and Bt. 40Ar/39Ar geochronology on the amphibole dated one level to 2.24 ± 0.06 Ma, indicating the Late Pliocene. The grain size (fine ash) and textural features of the deposits are typical of pyroclastic fall deposits related to explosive eruptions with consequent upward projection of the fragmented material through Plinian columms. The columns turned eastward because of stratospheric winds and the material fell in a marine environment. It deposited on the slope of Pliocene basins in the frontal sector of the Southern Apennine chain. Structural features are the following: fining-upward gradation of the deposits with cross- and convolute laminations at the base and fine-grained massive beds at the top. They suggest that the primary pyroclastic fall deposits were mobilized as volcaniclastic turbidity currents towards a deeper environment. Glass and crystal compositions were investigated by SEM/EDS analysis. Petrographycal and chemical compositions of the

Allele Re-sequencing Technologies

DEFF Research Database (Denmark)

Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

2013-01-01

The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

Design of Long Period Pseudo-Random Sequences from the Addition of -Sequences over

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Ren Jian

2004-01-01

Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of -sequences with pairwise-prime linear spans (AMPLS. Using -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to , a signal set is constructed.

Significado estratigráfico y tectónico de los complejos de bloques resedimentados cambro-ordovicios de la Precordillera Occidental, Argentina

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Vaccari, N. E.

1992-12-01

Full Text Available Rocks belonging to the Early Paleozoic Los Sombreros Formation crop out on the eastern flank of the Sierra de Yerba Loca, along the Río Jáchal section. This Formation consists of black shales and turbidites with interbedded limestone boulders near the base of the section, one of them up to 200 m long and 30 m thick. Boulders yield both early Cambrian trilobites and early Ordovician conodonts. Near the top, a thick sequence of dark grey marls and limestone contains an early Middle Cambrian trilobite fauna which is overlain by limestone and calcareous turbidites containing early Llanvirn graptolites and conodonts. On the basis of paleontological and sedimentological evidences this sequence can be interpreted as a series of submarine gravity slides interbedded within a dominantly turbiditic sequence. The Cambrian-early Ordovician precordilleran carbonate platform served as the source for much of the sediment which was redeposited on the slope. Then, deposition of the early Ordovician Los Sombreros Formation could be related to uplift and erosion of the platform margin and steeping of the slope during the late Arenig-early Llanvirn.En el flanco oriental de la Sierra de Yerba Loca, sobre el corte del río Jáchal, aflora una secuencia de edad paleozoica temprana correspondiente a los afloramientos más septentrionales de la Formación Los Sombreros. Esta unidad se compone de lutitas negras y turbiditas que contienen cerca de su base y hacia el techo horizontes de bloques calcáreos, algunos de enormes dimensiones -cerca de 30 m de espesor por más de 200 m de longitud- cuya fauna de trilobites y conodontos indica una edad Cámbrica y Ordovícica temprana. Hacia el techo de la sección está expuesta una potente secuencia de calcipelitas y calizas oscuras que contienen una fauna de trilobites del Cámbrico Medio basal, que es cubierta por brechas calcáreas y calciturbiditas portadoras de conodontos y graptolitos de edad llanvirniana temprana. Esta

Error Analysis of Deep Sequencing of Phage Libraries: Peptides Censored in Sequencing

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Wadim L. Matochko

2013-01-01

Full Text Available Next-generation sequencing techniques empower selection of ligands from phage-display libraries because they can detect low abundant clones and quantify changes in the copy numbers of clones without excessive selection rounds. Identification of errors in deep sequencing data is the most critical step in this process because these techniques have error rates >1%. Mechanisms that yield errors in Illumina and other techniques have been proposed, but no reports to date describe error analysis in phage libraries. Our paper focuses on error analysis of 7-mer peptide libraries sequenced by Illumina method. Low theoretical complexity of this phage library, as compared to complexity of long genetic reads and genomes, allowed us to describe this library using convenient linear vector and operator framework. We describe a phage library as N×1 frequency vector n=ni, where ni is the copy number of the ith sequence and N is the theoretical diversity, that is, the total number of all possible sequences. Any manipulation to the library is an operator acting on n. Selection, amplification, or sequencing could be described as a product of a N×N matrix and a stochastic sampling operator (Sa. The latter is a random diagonal matrix that describes sampling of a library. In this paper, we focus on the properties of Sa and use them to define the sequencing operator (Seq. Sequencing without any bias and errors is Seq=Sa IN, where IN is a N×N unity matrix. Any bias in sequencing changes IN to a nonunity matrix. We identified a diagonal censorship matrix (CEN, which describes elimination or statistically significant downsampling, of specific reads during the sequencing process.

Late Glacial and Holocene gravity deposits in the Gulf of Lions deep basin, Western Mediterranean

Science.gov (United States)

Dennielou, B.; Bonnel, C.; Sultan, N.; Voisset, M.; Berné, S.; Beaudouin, C.; Guichard, F.; Melki, T.; Méar, Y.; Droz, L.

2003-04-01

Recent investigations in the Gulf of Lions have shown that complex gravity processes and deposits occurred in the deep basin since the last Glacial period. Besides the largest western Mediterranean turbiditic system, Petit-Rhône deep-sea fan (PRDSF), whose built-up started at the end of Pliocene, several sedimentary bodies can be distinguished: (1) The turbiditic Pyreneo-Languedocian ridge (PLR), at the outlet of the Sète canyon network, whose activity is strongly connected to the sea level and the connection of the canyons with the rivers. It surface shows long wave-length sediment waves, probably in relation with the turbiditic overspill. (2) An acoustically chaotic unit, filling the topographic low between the PRDSF and the PLR, the Lower Interlobe Unit. Possible source areas are the Sète canyon and/or the Marti Canyon. (3) An acoustically transparent unit, below the neofan, filling the same topographic low, the Western Transparent Unit, interpreted as a debris-flow. Recent sediment cores have shown that this sedimentary is composed of folded, laminated mud, both in its northern and southern fringes. (4) The Petit-Rhône neofan, a channelized turbiditic lobe resulting from the last avulsion of the Petit-Rhône turbiditic channel and composed of two units. The lower, acoustically chaotic facies unit, corresponding to an initial stage of the avulsion, similar to the HARP facies found on the Amazon fan. The upper, transparent, slightly bedded, channel-levee shaped unit, corresponding to the channelized stage of the avulsion. (5) Up to ten, Deglacial to Holocene, thin, fine sand layers, probably originating from shelf-break sand accumulations, through the Sète canyon network. (6) Giant scours, in the southern, distal part of the neofan, possibly linked to turbiditic overflow from the neo-channel, probably corresponding to channel-lobe transition zone features (Wynn et al. 2002). Recent investigations have shown no evidence of bottom current features.

Log-balanced combinatorial sequences

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Tomislav Došlic

2005-01-01

Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

Testing 8000 years of submarine paleoseismicity record offshore western Algeria : First evidence for irregular seismic cycles

Science.gov (United States)

Ratzov, G.; Cattaneo, A.; Babonneau, N.; Yelles, K.; Bracene, R.; Deverchere, J.

2012-12-01

It is commonly assumed that stress buildup along a given fault is proportional to the time elapsed since the previous earthquake. Although the resulting « seismic gap » hypothesis suits well for moderate magnitude earthquakes (Mw 4-5), large events (Mw>6) are hardly predictable and depict great variation in recurrence intervals. Models based on stress transfer and interactions between faults argue that an earthquake may promote or delay the occurrence of next earthquakes on adjacent faults by increasing or lowering the level of static stress. The Algerian margin is a Cenozoic passive margin presently inverted within the slow convergence between Africa and Eurasia plates (~3-6 mm/yr). The western margin experienced two large earthquakes in 1954 (Orléansville, M 6.7) and 1980 (El Asnam, M 7.3), supporting an interaction between the two faults. To get meaningful statistics of large earthquakes recurrence intervals over numerous seismic cycles, we conducted a submarine paleoseismicity investigation based on turbidite chronostratigraphy. As evidenced on the Cascadia subduction zone, synchronous turbidites accumulated over a large area and originated from independent sources are likely triggered by an earthquake. To test the method on a slowly convergent margin, we analyze turbidites from three sediment cores collected during the Maradja (2003) and Prisme (2007) cruises off the 1954-1980 source areas. We use X-ray radioscopy, XRF major elements counter, magnetic susceptibility, and grain-size distribution to accurately discriminate turbidites from hemipelagites. We date turbidites by calculating hemipelagic sedimentation rates obtained with radiocarbon ages, and interpolate the rates between turbidites. Finally, the age of events is compared with the only paleoseismic study available on land (El Asnam fault). Fourteen possible seismic events are identified by the counting and correlation of turbidites over the last 8 ka. Most events are correlated with the

Seismoturbidite record as preserved at core sites at the Cascadia and Sumatra–Andaman subduction zones

Directory of Open Access Journals (Sweden)

J. R. Patton

2013-04-01

Full Text Available Turbidite deposition along slope and trench settings is evaluated for the Cascadia and Sumatra–Andaman subduction zones. Source proximity, basin effects, turbidity current flow path, temporal and spatial earthquake rupture, hydrodynamics, and topography all likely play roles in the deposition of the turbidites as evidenced by the vertical structure of the final deposits. Channel systems tend to promote low-frequency components of the content of the current over longer distances, while more proximal slope basins and base-of-slope apron fan settings result in a turbidite structure that is likely influenced by local physiography and other factors. Cascadia's margin is dominated by glacial cycle constructed pathways which promote turbidity current flows for large distances. Sumatra margin pathways do not inherit these antecedent sedimentary systems, so turbidity currents are more localized.

Clinical evaluation of further-developed MRCP sequences in comparison with standard MRCP sequences

International Nuclear Information System (INIS)

Hundt, W.; Scheidler, J.; Reiser, M.; Petsch, R.

2002-01-01

The purpose of this study was the comparison of technically improved single-shot magnetic resonance cholangiopancreatography (MRCP) sequences with standard single-shot rapid acquisition with relaxation enhancement (RARE) and half-Fourier acquired single-shot turbo spin-echo (HASTE) sequences in evaluating the normal and abnormal biliary duct system. The bile duct system of 45 patients was prospectively investigated on a 1.5-T MRI system. The investigation was performed with RARE and HASTE MR cholangiography sequences with standard and high spatial resolutions, and with a delayed-echo half-Fourier RARE (HASTE) sequence. Findings of the improved MRCP sequences were compared with the standard MRCP sequences. The level of confidence in assessing the diagnosis was divided into five groups. The Wilcoxon signed-rank test at a level of p<0.05 was applied. In 15 patients no pathology was found. The MRCP showed stenoses of the bile duct system in 10 patients and choledocholithiasis and cholecystolithiasis in 16 patients. In 12 patients a dilatation of the bile duct system was found. Comparison of the low- and high spatial resolution sequences and the short and long TE times of the half-Fourier RARE (HASTE) sequence revealed no statistically significant differences regarding accuracy of the examination. The diagnostic confidence level in assessing normal or pathological findings for the high-resolution RARE and half-Fourier RARE (HASTE) was significantly better than for the standard sequences. For the delayed-echo half-Fourier RARE (HASTE) sequence no statistically significant difference was seen. The high-resolution RARE and half-Fourier RARE (HASTE) sequences had a higher confidence level, but there was no significant difference in diagnosis in terms of detection and assessment of pathological changes in the biliary duct system compared with standard sequences. (orig.)

Polyadenylated Sequencing Primers Enable Complete Readability of PCR Amplicons Analyzed by Dideoxynucleotide Sequencing

Directory of Open Access Journals (Sweden)

Martin Beránek

2012-01-01

Full Text Available Dideoxynucleotide DNA sequencing is one of the principal procedures in molecular biology. Loss of an initial part of nucleotides behind the 3' end of the sequencing primer limits the readability of sequenced amplicons. We present a method which extends the readability by using sequencing primers modified by polyadenylated tails attached to their 5' ends. Performing a polymerase chain reaction, we amplified eight amplicons of six human genes (AMELX, APOE, HFE, MBL2, SERPINA1 and TGFB1 ranging from 106 bp to 680 bp. Polyadenylation of the sequencing primers minimized the loss of bases in all amplicons. Complete sequences of shorter products (AMELX 106 bp, SERPINA1 121 bp, HFE 208 bp, APOE 244 bp, MBL2 317 bp were obtained. In addition, in the case of TGFB1 products (366 bp, 432 bp, and 680 bp, respectively, the lengths of sequencing readings were significantly longer if adenylated primers were used. Thus, single strand dideoxynucleotide sequencing with adenylated primers enables complete or near complete readability of short PCR amplicons.

Mixed Sequence Reader: A Program for Analyzing DNA Sequences with Heterozygous Base Calling

Science.gov (United States)

Chang, Chun-Tien; Tsai, Chi-Neu; Tang, Chuan Yi; Chen, Chun-Houh; Lian, Jang-Hau; Hu, Chi-Yu; Tsai, Chia-Lung; Chao, Angel; Lai, Chyong-Huey; Wang, Tzu-Hao; Lee, Yun-Shien

2012-01-01

The direct sequencing of PCR products generates heterozygous base-calling fluorescence chromatograms that are useful for identifying single-nucleotide polymorphisms (SNPs), insertion-deletions (indels), short tandem repeats (STRs), and paralogous genes. Indels and STRs can be easily detected using the currently available Indelligent or ShiftDetector programs, which do not search reference sequences. However, the detection of other genomic variants remains a challenge due to the lack of appropriate tools for heterozygous base-calling fluorescence chromatogram data analysis. In this study, we developed a free web-based program, Mixed Sequence Reader (MSR), which can directly analyze heterozygous base-calling fluorescence chromatogram data in .abi file format using comparisons with reference sequences. The heterozygous sequences are identified as two distinct sequences and aligned with reference sequences. Our results showed that MSR may be used to (i) physically locate indel and STR sequences and determine STR copy number by searching NCBI reference sequences; (ii) predict combinations of microsatellite patterns using the Federal Bureau of Investigation Combined DNA Index System (CODIS); (iii) determine human papilloma virus (HPV) genotypes by searching current viral databases in cases of double infections; (iv) estimate the copy number of paralogous genes, such as β-defensin 4 (DEFB4) and its paralog HSPDP3. PMID:22778697

The Salinas formation in the type-area, Northeastern Minas Gerais: a proposal to review the stratigraphy of the Aracuai belt on sedimentary, metamorphic and U-Pb SHRIMP evidences

International Nuclear Information System (INIS)

Lima, Sirlene A. de Abreu; Pedrosa Soares, Antonio C.; Cordani, Umberto G.; Nutman, Allen

2002-01-01

The Salinas Formation has been considered to be a stratigraphic unit of the Macaubas Group. This group comprises the rift to passive margin sequences of the precursor basin of the Neo proterozoic Aracuai Orogeny, eastern Brazil. However, new road cuts show extensive and spectacular outcrops with very well-preserved sedimentary structures, allowing detailed studies in the type-locality of this formation, located in the Salinas town and surroundings, northeast Minas Gerais State. In its type-locality, the Salinas Formation consists of graywacke, pelite and clast-supported conglomerate, metamorphosed in the green schist facies. The sedimentary lithofacies are grouped into three facies association (shelf, slope and deep-sea), indicating sedimentation from shelf deposits to deep-water turbidites. The shelf sedimentation was influenced by storm-wave during deposition. The slump and deep-sea deposits were generated by gravitational flows and high- to low-concentration turbidity currents. Shelf sandstone, clast-supported conglomerate and proximal to distal turbidites outline a submarine fan system. U-Pb SHRIMP data from detrital zircons of graywacke samples indicate a maximum sedimentation age of ca. 568 Ma. Thus, the Salinas Formation is much younger than the Macaubas Group, and represents late orogenic deposits (ca. 568- 500 Ma). The distal, passive margin unit of the Macaubas Group is now called Ribeirao da Folha Formation (ca. 800 Ma). (author)

Sequence Read Archive (SRA)

Data.gov (United States)

U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.

Science.gov (United States)

Huber, Thomas; Faulkner, Geoffrey; Hugenholtz, Philip

2004-09-22

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl

DEPOSITIONAL ENVIRONMENTS OF SUPRACRUSTAL METASEDIMENTARY SEQUENCE AND POSSIBLE MODEL FOR ZINC MINERALIZATION OF RIO CLARO AREA, RIO DE JANEIRO STATE (BRAZIL

Directory of Open Access Journals (Sweden)

Ronaldo Mello Pereira

2016-10-01

Full Text Available This work focuses on Neoproterozoic supracrustal rocks related to Andrelandia megasequence, which are superimposed on the basis represented by neoarchean granulites and palaeoproterozoic ortogneiss, in order to define palaeoenvironments of deposition of metasedimentary rocks and typological model of zinc mineralization of Rio Claro, Rio de Janeiro State, SE of Brazil. Three stratigraphic units in the area were considered for the studies: Valadão, São Roque and Lidice. Valadão unit was divided into three subunits: psamitic, psamitic / pelitic and pelitic. On the whole, it represents a turbiditic sequence influenced by underwater hydrothermal exhalations that led to the formation of quartzite with magnetite, considered as banded iron formations. São Roque Unit is composed of four subunits (São Roque I, II, III and IV and presents a typical pattern of deposition of low energy environments, in marine deep basins. Gondite, coticules levels and (Mn-almandine present in the local gneiss mark the manganese exalative contribution in that unit. Lídice unit has different sedimentation palaeoenvironments and is subdivided into Lídice I, II and III. Lídice subunits I and II exhibit quartzite interleaved with pelitic rocks and graphite gneiss, suggesting deposition in deeper environments of the basin, probably related to turbidity currents. In Lídice III subunit, more carbonated and with more quartz, limestone quartzite stand out, which enclose mineralized zones, reflecting depositional environment in shallow platform, possibly involving evaporitic environment, sabkha type. Sulfite mineralization of Rio Claro, associated with platformal rocks intensely metamorphosed and deformed, as well as its local geological context, features similarities with sedimentary exhalative deposits (SEDEX Zn-Pb-Ag model, Shuswap and Monashee type, present in Monashee and Shuswap Complexes of British Columbia in Canada.

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

DEFF Research Database (Denmark)

de Souza, S J; Camargo, A A; Briones, M R

2000-01-01

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central ...

Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

Science.gov (United States)

Martin, Andrew C R

2014-01-01

The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing

Directory of Open Access Journals (Sweden)

Miri eMichaeli

2012-12-01

Full Text Available High throughput sequencing (HTS yields tens of thousands to millions of sequences that require a large amount of pre-processing work to clean various artifacts. Such cleaning cannot be performed manually. Existing programs are not suitable for immunoglobulin (Ig genes, which are variable and often highly mutated. This paper describes Ig-HTS-Cleaner (Ig High Throughput Sequencing Cleaner, a program containing a simple cleaning procedure that successfully deals with pre-processing of Ig sequences derived from HTS, and Ig-Indel-Identifier (Ig Insertion – Deletion Identifier, a program for identifying legitimate and artifact insertions and/or deletions (indels. Our programs were designed for analyzing Ig gene sequences obtained by 454 sequencing, but they are applicable to all types of sequences and sequencing platforms. Ig-HTS-Cleaner and Ig-Indel-Identifier have been implemented in Java and saved as executable JAR files, supported on Linux and MS Windows. No special requirements are needed in order to run the programs, except for correctly constructing the input files as explained in the text. The programs' performance has been tested and validated on real and simulated data sets.

Lithofacies control in detrital zircon provenance studies: Insights from the Cretaceous Methow basin, southern Canadian Cordillera

Science.gov (United States)

DeGraaff-Surpless, K.; Mahoney, J.B.; Wooden, J.L.; McWilliams, M.O.

2003-01-01

High-frequency sampling for detrital zircon analysis can provide a detailed record of fine-scale basin evolution by revealing the temporal and spatial variability of detrital zircon ages within clastic sedimentary successions. This investigation employed detailed sampling of two sedimentary successions in the Methow/Methow-Tyaughton basin of the southern Canadian Cordillera to characterize the heterogeneity of detrital zircon signatures within single lithofacies and assess the applicability of detrital zircon analysis in distinguishing fine-scale provenance changes not apparent in lithologic analysis of the strata. The Methow/Methow-Tyaughton basin contains two distinct stratigraphic sequences of middle Albian to Santonian clastic sedimentary rocks: submarine-fan deposits of the Harts Pass Formation/Jackass Mountain Group and fluvial deposits of the Winthrop Formation. Although both stratigraphic sequences displayed consistent ranges in detrital zircon ages on a broad scale, detailed sampling within each succession revealed heterogeneity in the detrital zircon age distributions that was systematic and predictable in the turbidite succession but unpredictable in the fluvial succession. These results suggest that a high-density sampling approach permits interpretation of finescale changes within a lithologically uniform turbiditic sedimentary succession, but heterogeneity within fluvial systems may be too large and unpredictable to permit accurate fine-scale characterization of the evolution of source regions. The robust composite detrital zircon age signature developed for these two successions permits comparison of the Methow/Methow-Tyaughton basin age signature with known plutonic source-rock ages from major plutonic belts throughout the Cretaceous North American margin. The Methow/Methow-Tyaughton basin detrital zircon age signature matches best with source regions in the southern Canadian Cordillera, requiring that the basin developed in close proximity to the

Lower Paleozoic deep-water facies of the Medfra area, central Alaska: A section in Geologic studies in Alaska by the U.S. Geological Survey, 1997

Science.gov (United States)

Dumoulin, Julie A.; Bradley, Dwight C.; Harris, Anita G.; Repetski, John E.

1999-01-01

Deep-water facies, chiefly hemipelagic deposits and turbidites, of Cambrian through Devonian age are widely exposed in the Medfra and Mt. McKinley quadrangles. These strata include the upper part of the Telsitna Formation (Middle-Upper Ordovician) and the Paradise Fork Formation (Lower Silurian-Lower Devonian) in the Nixon Fork terrane, the East Fork Hills Formation (Upper Cambrian-Lower Devonian) in the East Fork subterrane of the Minchumina terrane, and the chert and argillite unit (Ordovician) and the argillite and quartzite unit (Silurian- Devonian? and possibly older) in the Telida subterrane of the Minchumina terrane.In the western part of the study area (Medfra quadrangle), both hemipelagic deposits and turbidites are largely calcareous and were derived from the Nixon Fork carbonate platform. East- ern exposures (Mt. McKinley quadrangle; eastern part of the Telida subterrane) contain much less carbonate; hemipelagic strata are mostly chert, and turbidites contain abundant rounded quartz and lesser plagioclase and potassium feldspar. Deep-water facies in the Medfra quadrangle correlate well with rocks of the Dillinger terrane exposed to the south (McGrath quadrangle), but coeval strata in the Mt. McKinley quadrangle are compositionally similar to rocks to the northeast (Livengood quadrangle). Petrographic data thus suggest that the Telida subterranes presently defined is an artificial construct made up of two distinct sequences of disparate provenance.Restoration of 90 and 150 km of dextral strike-slip on the Iditarod and Farewell faults, respectively, aligns the deep-water strata of the Minchumina and Dillinger terranes in a position east of the Nixon Fork carbonate platform. This restoration supports the interpretation that lower Paleozoic rocks in the Nixon Fork and Dillinger terranes, and in the western part of the Minchumina terrane (East Fork subterrane and western part of the Telida subterrane), formed along a single continental margin. Rocks in the

Multilocus Sequence Analysis and rpoB Sequencing of Mycobacterium abscessus (Sensu Lato) Strains▿

Science.gov (United States)

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-01-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536T, M. massiliense CIP 108297T, and M. bolletii CIP 108541T) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering

Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.

Science.gov (United States)

Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

2011-02-01

Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the

ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS

Directory of Open Access Journals (Sweden)

Alves-Ferreira Marcelo

2008-09-01

Full Text Available Abstract Background Genome survey sequences (GSS offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive regions of the genome. A more precise estimation of the nature, quantity and variability of repetitive sequences very early in a genome sequencing project is of considerable importance, as such data strongly influence the estimation of genome coverage, library quality and progress in scaffold construction. Also, the elimination of repetitive sequences from the initial assembly process is important to avoid errors and unnecessary complexity. Repetitive sequences are also of interest in a variety of other studies, for instance as molecular markers. Results We designed and implemented a straightforward pipeline called ReRep, which combines bioinformatics tools for identifying repetitive structures in a GSS dataset. In a case study, we first applied the pipeline to a set of 970 GSSs, sequenced in our laboratory from the human pathogen Leishmania braziliensis, the causative agent of leishmaniosis, an important public health problem in Brazil. We also verified the applicability of ReRep to new sequencing technologies using a set of 454-reads of an Escheria coli. The behaviour of several parameters in the algorithm is evaluated and suggestions are made for tuning of the analysis. Conclusion The ReRep approach for identification of repetitive elements in GSS datasets proved to be straightforward and efficient. Several potential repetitive sequences were found in a L. braziliensis GSS dataset generated in our laboratory, and further validated by the analysis of a more complete genomic dataset from the EMBL and Sanger Centre databases. ReRep also identified most of the E. coli K12 repeats prior to assembly in an example dataset obtained by automated sequencing using 454 technology. The parameters controlling the algorithm behaved consistently and may be tuned to the properties

sequenceMiner algorithm

Data.gov (United States)

National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics.

Science.gov (United States)

Harvey, Michael G; Smith, Brian Tilston; Glenn, Travis C; Faircloth, Brant C; Brumfield, Robb T

2016-09-01

Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of

Morphology, processes and geohazards of giant landslides in and around Agadir Canyon, northwest Africa - Cruise MSM32 - September 25 - October 30, 2013 - Bremen (Germany) - Cádiz (Spain)

OpenAIRE

Krastel, Sebastian; Böttner, Christof; Cartigny, Matthieu; Feldens, Peter; Fu, Lili; Glogowski, Silke; Guggolz, Theresa; Hellmann, Sebastian; Hühnerbach, Veit; Jähmlich, Heiko; Kraus, Katrin; Kretschmer, Jacob; Matthew, Duncan; Meier, Daniela; Mücke, Isabell

2014-01-01

Agadir Canyon is one of the largest submarine canyons in the World, supplying giant submarine sediment gravity flows to the Agadir Basin and the wider Moroccan Turbidite System. While the Moroccan Turbidite System is extremely well investigated, almost no data from the source region, i.e. the Agadir Canyon, are available. Understanding why some submarine landslides remain as coherent blocks of sediment throughout their passage downslope, while others mix and disintegrate almost immediately af...

A few Smarandache Integer Sequences

OpenAIRE

Ibstedt, Henry

2010-01-01

This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics

Science.gov (United States)

2012-01-01

Background The detection of conserved residue clusters on a protein structure is one of the effective strategies for the prediction of functional protein regions. Various methods, such as Evolutionary Trace, have been developed based on this strategy. In such approaches, the conserved residues are identified through comparisons of homologous amino acid sequences. Therefore, the selection of homologous sequences is a critical step. It is empirically known that a certain degree of sequence divergence in the set of homologous sequences is required for the identification of conserved residues. However, the development of a method to select homologous sequences appropriate for the identification of conserved residues has not been sufficiently addressed. An objective and general method to select appropriate homologous sequences is desired for the efficient prediction of functional regions. Results We have developed a novel index to select the sequences appropriate for the identification of conserved residues, and implemented the index within our method to predict the functional regions of a protein. The implementation of the index improved the performance of the functional region prediction. The index represents the degree of conserved residue clustering on the tertiary structure of the protein. For this purpose, the structure and sequence information were integrated within the index by the application of spatial statistics. Spatial statistics is a field of statistics in which not only the attributes but also the geometrical coordinates of the data are considered simultaneously. Higher degrees of clustering generate larger index scores. We adopted the set of homologous sequences with the highest index score, under the assumption that the best prediction accuracy is obtained when the degree of clustering is the maximum. The set of sequences selected by the index led to higher functional region prediction performance than the sets of sequences selected by other sequence

Yeast genome sequencing:

DEFF Research Database (Denmark)

Piskur, Jure; Langkjær, Rikke Breinhold

2004-01-01

For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

Sequence Matters but How Exactly? A Method for Evaluating Activity Sequences from Data

Science.gov (United States)

Doroudi, Shayan; Holstein, Kenneth; Aleven, Vincent; Brunskill, Emma

2016-01-01

How should a wide variety of educational activities be sequenced to maximize student learning? Although some experimental studies have addressed this question, educational data mining methods may be able to evaluate a wider range of possibilities and better handle many simultaneous sequencing constraints. We introduce Sequencing Constraint…

Environmental and human impact on the sedimentary dynamic in the Rhone Delta subaquatic canyons (France-Switzerland)

Science.gov (United States)

Arantegui, A.; Corella, J. P.; Loizeau, J. L.; Anselmetti, F. S.; Girardclos, S.

2012-04-01

sediment dynamics during whether extreme flood events or mass-movements due to deltaic scarp failures. The active canyon shows a classic turbiditic system with frequent spillover processes in the canyon floor/levee complex. Geotechnical measurements, a decrease in the frequency of turbidites and a fining upward sequence along the levee suggest that erosion dominates sedimentation in the canyon floor, while sedimentation dominates in the rapid levee building-up process, with sedimentation rates that exceed 3cm/yr in the proximal areas. Therefore, mechanisms controlling the sedimentary evolution on the active canyon result in a complex interplay between erosion and sedimentation. Further research will provide a detailed evaluation of the human impact on sedimentary dynamic in the Rhone Delta subaquatic canyons.

Mapping sequences by parts

Directory of Open Access Journals (Sweden)

Guziolowski Carito

2007-09-01

Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

From Sequence to Morphology - Long-Range Correlations in Complete Sequenced Genomes

NARCIS (Netherlands)

T.A. Knoch (Tobias)

2004-01-01

textabstractThe largely unresolved sequential organization, i.e. the relations within DNA sequences, and its connection to the three-dimensional organization of genomes was investigated by correlation analyses of completely sequenced chromosomes from Viroids, Archaea, Bacteria, Arabidopsis

Biomolecule Sequencer: Next-Generation DNA Sequencing Technology for In-Flight Environmental Monitoring, Research, and Beyond

Science.gov (United States)

Smith, David J.; Burton, Aaron; Castro-Wallace, Sarah; John, Kristen; Stahl, Sarah E.; Dworkin, Jason Peter; Lupisella, Mark L.

2016-01-01

On the International Space Station (ISS), technologies capable of rapid microbial identification and disease diagnostics are not currently available. NASA still relies upon sample return for comprehensive, molecular-based sample characterization. Next-generation DNA sequencing is a powerful approach for identifying microorganisms in air, water, and surfaces onboard spacecraft. The Biomolecule Sequencer payload, manifested to SpaceX-9 and scheduled on the Increment 4748 research plan (June 2016), will assess the functionality of a commercially-available next-generation DNA sequencer in the microgravity environment of ISS. The MinION device from Oxford Nanopore Technologies (Oxford, UK) measures picoamp changes in electrical current dependent on nucleotide sequences of the DNA strand migrating through nanopores in the system. The hardware is exceptionally small (9.5 x 3.2 x 1.6 cm), lightweight (120 grams), and powered only by a USB connection. For the ISS technology demonstration, the Biomolecule Sequencer will be powered by a Microsoft Surface Pro3. Ground-prepared samples containing lambda bacteriophage, Escherichia coli, and mouse genomic DNA, will be launched and stored frozen on the ISS until experiment initiation. Immediately prior to sequencing, a crew member will collect and thaw frozen DNA samples, connect the sequencer to the Surface Pro3, inject thawed samples into a MinION flow cell, and initiate sequencing. At the completion of the sequencing run, data will be downlinked for ground analysis. Identical, synchronous ground controls will be used for data comparisons to determine sequencer functionality, run-time sequence, current dynamics, and overall accuracy. We will present our latest results from the ISS flight experiment the first time DNA has ever been sequenced in space and discuss the many potential applications of the Biomolecule Sequencer for environmental monitoring, medical diagnostics, higher fidelity and more adaptable Space Biology Human

Pairwise Sequence Alignment Library

Energy Technology Data Exchange (ETDEWEB)

2015-05-20

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

Upper Cretaceous chalk facies and depositional history recorded in the Mona-1 core, Mona Ridge, Danish North Sea

Directory of Open Access Journals (Sweden)

Finn Surlyk

2011-12-01

Full Text Available The 331 m long core from the Mona-1 well in the Danish North Sea spans almost the entire Upper Cretaceous Chalk Group but only about 10% of Late Cretaceous time is represented. The succession comprises 14 facies representing pelagic deposition, turbidity flow, and mass-transport processes, including mudflow, debris flow, and slumping. Pelagic deposits vary mainly in terms of the concentration of siliciclastic material, the trace-fossil assemblage, and the presence or ab¬sence of primary sedimentary structures. Pelagic sedimentation was probably punctuated by the deposition of thin turbidites, and the resultant deposits were thoroughly bioturbated if deposited during normal oxygenation at the sea floor. Periodic benthic dysoxia resulted in the preservation of primary structures, as represented by laminated chalk which consists of thin pelagic laminae alternating with thin turbidites. In addition to the thin turbidites in the laminated chalk, four dif¬ferent turbidite facies are interpreted as representing high- to low-energy flows. Clast-supported chalk conglomerates have previously not been differentiated from other turbidites, but are here interpreted to be directly related to the down-slope evolution of debris flows. Debris flows are rep¬resented by matrix-supported conglomerates, which form one of the most common facies in the succession. High-concentration, gravity-driven suspension flows passed into dilute visco-plastic flows during the final stages of deposition and resulted in the deposition of structureless chalks. Limited shear deformation produced distinct quasi-facies from which the precursor facies can be deduced, whereas intense or continued shear deformation produced a shear-banded quasi-facies from which the precursor facies cannot be deduced in all cases. A series of major slump packages (14–18 in total are interpreted, forming over 40% of the succession; debrites appear to be the most common precursor facies involved in

Upper Cretaceous chalk facies and depositional history recorded in the Mona-1 core, Mona Ridge, Danish North Sea: Plate 1

Directory of Open Access Journals (Sweden)

Surlyk, Finn

2011-12-01

Full Text Available The 331 m long core from the Mona-1 well in the Danish North Sea spans almost the entire Upper Cretaceous Chalk Group but only about 10% of Late Cretaceous time is represented. The succession comprises 14 facies representing pelagic deposition, turbidity flow, and mass-transport processes, including mudflow, debris flow, and slumping. Pelagic deposits vary mainly in terms of the concentration of siliciclastic material, the trace-fossil assemblage, and the presence or ab¬sence of primary sedimentary structures. Pelagic sedimentation was probably punctuated by the deposition of thin turbidites, and the resultant deposits were thoroughly bioturbated if deposited during normal oxygenation at the sea floor. Periodic benthic dysoxia resulted in the preservation of primary structures, as represented by laminated chalk which consists of thin pelagic laminae alternating with thin turbidites. In addition to the thin turbidites in the laminated chalk, four dif¬ferent turbidite facies are interpreted as representing high- to low-energy flows. Clast-supported chalk conglomerates have previously not been differentiated from other turbidites, but are here interpreted to be directly related to the down-slope evolution of debris flows. Debris flows are rep¬resented by matrix-supported conglomerates, which form one of the most common facies in the succession. High-concentration, gravity-driven suspension flows passed into dilute visco-plastic flows during the final stages of deposition and resulted in the deposition of structureless chalks. Limited shear deformation produced distinct quasi-facies from which the precursor facies can be deduced, whereas intense or continued shear deformation produced a shear-banded quasi-facies from which the precursor facies cannot be deduced in all cases. A series of major slump packages (14–18 in total are interpreted, forming over 40% of the succession; debrites appear to be the most common precursor facies involved in

Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

Directory of Open Access Journals (Sweden)

Stephan Pabinger

Full Text Available Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM. Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage

DNA Sequencing by Capillary Electrophoresis

Science.gov (United States)

Karger, Barry L.; Guttman, Andras

2009-01-01

Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

HIV Sequence Compendium 2015

Energy Technology Data Exchange (ETDEWEB)

Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2015-10-05

This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

PN Sequence Preestimator Scheme for DS-SS Signal Acquisition Using Block Sequence Estimation

Directory of Open Access Journals (Sweden)

Sang Kyu Park

2005-03-01

Full Text Available An m-sequence (PN sequence preestimator scheme for direct-sequence spread spectrum (DS-SS signal acquisition by using block sequence estimation (BSE is proposed and analyzed. The proposed scheme consists of an estimator and a verifier which work according to the PN sequence chip clock, and provides not only the enhanced chip estimates with a threshold decision logic and one-chip error correction among the first m received chips, but also the reliability check of the estimates with additional decision logic. The probabilities of the estimator and verifier operations are calculated. With these results, the detection, the false alarm, and the missing probabilities of the proposed scheme are derived. In addition, using a signal flow graph, the average acquisition time is calculated. The proposed scheme can be used as a preestimator and easily implemented by changing the internal signal path of a generally used digital matched filter (DMF correlator or any other correlator that has a lot of sampling data memories for sampled PN sequence. The numerical results show rapid acquisition performance in a relatively good CNR.

Climate and sea level controlled sedimentation processes in two submarine canyons off NW-Africa

OpenAIRE

Pierau, Roberto

2008-01-01

This study focuses on the trigger mechanisms of gravity-driven sediment transport in two submarine canyons at the passive continental margin off NW-Africa during the past 240 kyr. The sedimentary records allow to determine the turbidite emplacement times based on high resolution age models. The sediment textures of the turbidites were studied by using X-ray radiographies. The sedimentary properties like the terrigenous silt size distribution and XRF-core scanning element data allow to identif...

GuiTope: an application for mapping random-sequence peptides to protein sequences.

Science.gov (United States)

Halperin, Rebecca F; Stafford, Phillip; Emery, Jack S; Navalkar, Krupa Arun; Johnston, Stephen Albert

2012-01-03

Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC) at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.

GuiTope: an application for mapping random-sequence peptides to protein sequences

Directory of Open Access Journals (Sweden)

Halperin Rebecca F

2012-01-01

Full Text Available Abstract Background Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequences to the natural protein binding partners to infer the exact binding site or the importance of particular residues. The ability to search a set of sequences for similarity to a set of peptides may sometimes enable the prediction of an antibody epitope or a novel binding partner. We have developed a software application designed specifically for this task. Results GuiTope provides a graphical user interface for aligning peptide sequences to protein sequences. All alignment parameters are accessible to the user including the ability to specify the amino acid frequency in the peptide library; these frequencies often differ significantly from those assumed by popular alignment programs. It also includes a novel feature to align di-peptide inversions, which we have found improves the accuracy of antibody epitope prediction from peptide microarray data and shows utility in analyzing phage display datasets. Finally, GuiTope can randomly select peptides from a given library to estimate a null distribution of scores and calculate statistical significance. Conclusions GuiTope provides a convenient method for comparing selected peptide sequences to protein sequences, including flexible alignment parameters, novel alignment features, ability to search a database, and statistical significance of results. The software is available as an executable (for PC at http://www.immunosignature.com/software and ongoing updates and source code will be available at sourceforge.net.

Targeted sequencing of plant genomes

Science.gov (United States)

Mark D. Huynh

2014-01-01

Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

Repdigits in k-Lucas sequences

Indian Academy of Sciences (India)

57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence ( L n ( 2 ) ) n . In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences ...

Enrichment of target sequences for next-generation sequencing applications in research and diagnostics.

Science.gov (United States)

Altmüller, Janine; Budde, Birgit S; Nürnberg, Peter

2014-02-01

Abstract Targeted re-sequencing such as gene panel sequencing (GPS) has become very popular in medical genetics, both for research projects and in diagnostic settings. The technical principles of the different enrichment methods have been reviewed several times before; however, new enrichment products are constantly entering the market, and researchers are often puzzled about the requirement to take decisions about long-term commitments, both for the enrichment product and the sequencing technology. This review summarizes important considerations for the experimental design and provides helpful recommendations in choosing the best sequencing strategy for various research projects and diagnostic applications.

HIV Sequence Compendium 2010

Energy Technology Data Exchange (ETDEWEB)

Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2010-12-31

This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

Almost convergence of triple sequences

OpenAIRE

Ayhan Esi; M.Necdet Catalbas

2013-01-01

In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

Sequence History Update Tool

Science.gov (United States)

Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

2008-01-01

The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

OpenAIRE

BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

2011-01-01

In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

The sequence specificity of UV-induced DNA damage in a systematically altered DNA sequence.

Science.gov (United States)

Khoe, Clairine V; Chung, Long H; Murray, Vincent

2018-06-01

The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification. Absorption of UV photons by DNA leads to dimerisation of pyrimidine bases and produces two major photoproducts, cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). A previous study had determined that two hexanucleotide sequences, 5'-GCTC*AC and 5'-TATT*AA, were high intensity UV-induced DNA damage sites. The UV clone plasmid was constructed by systematically altering each nucleotide of these two hexanucleotide sequences. One of the main goals of this study was to determine the influence of single nucleotide alterations on the intensity of UV-induced DNA damage. The sequence 5'-GCTC*AC was designed to examine the sequence specificity of 6-4PPs and the highest intensity 6-4PP damage sites were found at 5'-GTTC*CC nucleotides. The sequence 5'-TATT*AA was devised to investigate the sequence specificity of CPDs and the highest intensity CPD damage sites were found at 5'-TTTT*CG nucleotides. It was proposed that the tetranucleotide DNA sequence, 5'-YTC*Y (where Y is T or C), was the consensus sequence for the highest intensity UV-induced 6-4PP adduct sites; while it was 5'-YTT*C for the highest intensity UV-induced CPD damage sites. These consensus tetranucleotides are composed entirely of consecutive pyrimidines and must have a DNA conformation that is highly productive for the absorption of UV photons. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

"First generation" automated DNA sequencing technology.

Science.gov (United States)

Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

2011-10-01

Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

The recurrence sequences via Sylvester matrices

Science.gov (United States)

Karaduman, Erdal; Deveci, Ömür

2017-07-01

In this work, we define the Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by using the Slyvester matrices which are obtained from the characteristic polynomials of the Pell and Jacobsthal sequences and then, we study the sequences defined modulo m. Also, we obtain the cyclic groups and the semigroups from the generating matrices of these sequences when read modulo m and then, we derive the relationships among the orders of the cyclic groups and the periods of the sequences. Furthermore, we redefine Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by means of the elements of the groups and then, we examine them in the finite groups.

Swab-to-Sequence: Real-time Data Analysis Platform for the Biomolecule Sequencer

Data.gov (United States)

National Aeronautics and Space Administration — DNA was successfully sequenced on the ISS in 2016, but the DNA sequenced was prepared on the ground. With FY’16 IRAD funds, the same team developed a...

Quantitative phenotyping via deep barcode sequencing.

Science.gov (United States)

Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

2009-10-01

Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

ADDRESS SEQUENCES FOR MULTI RUN RAM TESTING

Directory of Open Access Journals (Sweden)

V. N. Yarmolik

2014-01-01

Full Text Available A universal approach for generation of address sequences with specified properties is proposed and analyzed. A modified version of the Antonov and Saleev algorithm for Sobol sequences genera-tion is chosen as a mathematical description of the proposed method. Within the framework of the proposed universal approach, the Sobol sequences form a subset of the address sequences. Other sub-sets are also formed, which are Gray sequences, anti-Gray sequences, counter sequences and sequenc-es with specified properties.

The advantages of SMRT sequencing

OpenAIRE

Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

2013-01-01

Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data.

Science.gov (United States)

Fernández-Caballero Rico, Jose Ángel; Chueca Porcuna, Natalia; Álvarez Estévez, Marta; Mosquera Gutiérrez, María Del Mar; Marcos Maeso, María Ángeles; García, Federico

2018-02-01

To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies. Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies. At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100). A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Rapid Diagnostics of Onboard Sequences

Science.gov (United States)

Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

2012-01-01

Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

MatrixPlot: visualizing sequence constraints

DEFF Research Database (Denmark)

Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

1999-01-01

MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...

Anomaly Detection in Sequences

Data.gov (United States)

National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

Direct, rapid RNA sequence analysis

International Nuclear Information System (INIS)

Peattie, D.A.

1987-01-01

The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

An evaluation of Comparative Genome Sequencing (CGS by comparing two previously-sequenced bacterial genomes

Directory of Open Access Journals (Sweden)

Herring Christopher D

2007-08-01

Full Text Available Abstract Background With the development of new technology, it has recently become practical to resequence the genome of a bacterium after experimental manipulation. It is critical though to know the accuracy of the technique used, and to establish confidence that all of the mutations were detected. Results In order to evaluate the accuracy of genome resequencing using the microarray-based Comparative Genome Sequencing service provided by Nimblegen Systems Inc., we resequenced the E. coli strain W3110 Kohara using MG1655 as a reference, both of which have been completely sequenced using traditional sequencing methods. CGS detected 7 of 8 small sequence differences, one large deletion, and 9 of 12 IS element insertions present in W3110, but did not detect a large chromosomal inversion. In addition, we confirmed that CGS also detected 2 SNPs, one deletion and 7 IS element insertions that are not present in the genome sequence, which we attribute to changes that occurred after the creation of the W3110 lambda clone library. The false positive rate for SNPs was one per 244 Kb of genome sequence. Conclusion CGS is an effective way to detect multiple mutations present in one bacterium relative to another, and while highly cost-effective, is prone to certain errors. Mutations occurring in repeated sequences or in sequences with a high degree of secondary structure may go undetected. It is also critical to follow up on regions of interest in which SNPs were not called because they often indicate deletions or IS element insertions.

Short read sequence typing (SRST: multi-locus sequence types from short reads

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Inouye Michael

2012-07-01

Full Text Available Abstract Background Multi-locus sequence typing (MLST has become the gold standard for population analyses of bacterial pathogens. This method focuses on the sequences of a small number of loci (usually seven to divide the population and is simple, robust and facilitates comparison of results between laboratories and over time. Over the last decade, researchers and population health specialists have invested substantial effort in building up public MLST databases for nearly 100 different bacterial species, and these databases contain a wealth of important information linked to MLST sequence types such as time and place of isolation, host or niche, serotype and even clinical or drug resistance profiles. Recent advances in sequencing technology mean it is increasingly feasible to perform bacterial population analysis at the whole genome level. This offers massive gains in resolving power and genetic profiling compared to MLST, and will eventually replace MLST for bacterial typing and population analysis. However given the wealth of data currently available in MLST databases, it is crucial to maintain backwards compatibility with MLST schemes so that new genome analyses can be understood in their proper historical context. Results We present a software tool, SRST, for quick and accurate retrieval of sequence types from short read sets, using inputs easily downloaded from public databases. SRST uses read mapping and an allele assignment score incorporating sequence coverage and variability, to determine the most likely allele at each MLST locus. Analysis of over 3,500 loci in more than 500 publicly accessible Illumina read sets showed SRST to be highly accurate at allele assignment. SRST output is compatible with common analysis tools such as eBURST, Clonal Frame or PhyloViz, allowing easy comparison between novel genome data and MLST data. Alignment, fastq and pileup files can also be generated for novel alleles. Conclusions SRST is a novel

Computational analysis of sequence selection mechanisms.

Science.gov (United States)

Meyerguz, Leonid; Grasso, Catherine; Kleinberg, Jon; Elber, Ron

2004-04-01

Mechanisms leading to gene variations are responsible for the diversity of species and are important components of the theory of evolution. One constraint on gene evolution is that of protein foldability; the three-dimensional shapes of proteins must be thermodynamically stable. We explore the impact of this constraint and calculate properties of foldable sequences using 3660 structures from the Protein Data Bank. We seek a selection function that receives sequences as input, and outputs survival probability based on sequence fitness to structure. We compute the number of sequences that match a particular protein structure with energy lower than the native sequence, the density of the number of sequences, the entropy, and the "selection" temperature. The mechanism of structure selection for sequences longer than 200 amino acids is approximately universal. For shorter sequences, it is not. We speculate on concrete evolutionary mechanisms that show this behavior.

Putting instruction sequences into effect

NARCIS (Netherlands)

Bergstra, J.A.

2011-01-01

An attempt is made to define the concept of execution of an instruction sequence. It is found to be a special case of directly putting into effect of an instruction sequence. Directly putting into effect of an instruction sequences comprises interpretation as well as execution. Directly putting into

Repeated DNA sequences in fungi

Energy Technology Data Exchange (ETDEWEB)

Dutta, S K

1974-11-01

Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

Chameleon sequences in neurodegenerative diseases.

Science.gov (United States)

Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

2016-03-25

Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

Chameleon sequences in neurodegenerative diseases

International Nuclear Information System (INIS)

Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

2016-01-01

Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

Chameleon sequences in neurodegenerative diseases

Energy Technology Data Exchange (ETDEWEB)

Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

2016-03-25

Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

Multineuronal Spike Sequences Repeat with Millisecond Precision

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Koki eMatsumoto

2013-06-01

Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

cis sequence effects on gene expression

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Jacobs Kevin

2007-08-01

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

Stratigraphy of Eocene Sediments in the Soutwest Thrace

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Muhsin SÜMENGEN

1991-06-01

Full Text Available The area concerned is situated in the Gelibolu peninsula, north of the Saros Bay and northwest of the Marmara sea sediments of Upper Cretaceous to Miocene age, having a variety of fades crop out SW of Thrace. During the present survey, the goal was to examine the stratigraphic features of the Eocene sediments in the region. The Tertiary basin is underlain by an ophiolitic complex emplaced prior to Maastrichtian and limestone of Maastrichtian to Palaeocene age. The base of the limestone is not exposed within the region. The Tertiary transgression began in the Early Eocene in the Gelibolu peninsula. Massive mudstones, sandstone sequences that become thicker and coarser upward, and channel fill sediments are the first products of this transgression (Karaağaç limanı formation. This sequence is overlain by deltaic sediments beginning with massive mudstones and becoming thicker and coarser upward (Koyun limanı formation. These sediments are conformably and transitionally overlain by interbedded mudstone and sandstone, cut by channel fill deposits (Rcitepe formation. This formation was formed by meandering rivers. The sea that progressed inward to the Gelibolu peninsula during the Early Eocene began to become shallower again at the beginning of Lutetian and as a result, the region as a whole became a positive area during the Middle Lutetian. During the Late Lutetian, a new transgression occurred in the entire region. The first product of this transgression was a limestone (Soğucak formation. This limestone which was deposited in a shallow sea environment is locally intercalated with sandstone and conglomerate. The sea became deeper from the beginning of Upper Eocene. Firstly, turbiditic sandstone, and mudstone interbedded hemipelagic mudstone (Gaziköy formation with tuff, and carbonate mudstone and massive mudstone (Burgaz formation were deposited. These units are products of flat basins. These are, in turn, overlain by sequences consisting of

DNA sequencing conference, 2

Energy Technology Data Exchange (ETDEWEB)

Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

1991-06-19

This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Science.gov (United States)

Olson, Nathan D.; Lund, Steven P.; Zook, Justin M.; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S.; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B.

2015-01-01

This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Directory of Open Access Journals (Sweden)

Nathan D. Olson

2015-03-01

Full Text Available This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1 identity of biologically conserved position, (2 ratio of 16S rRNA gene copies featuring identified variants, and (3 the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.

Comparison of two Next Generation sequencing platforms for full genome sequencing of Classical Swine Fever Virus

DEFF Research Database (Denmark)

Fahnøe, Ulrik; Pedersen, Anders Gorm; Höper, Dirk

2013-01-01

to the consensus sequence. Additionally, we got an average sequence depth for the genome of 4000 for the Iontorrent PGM and 400 for the FLX platform making the mapping suitable for single nucleotide variant (SNV) detection. The analysis revealed a single non-silent SNV A10665G leading to the amino acid change D......Next Generation Sequencing (NGS) is becoming more adopted into viral research and will be the preferred technology in the years to come. We have recently sequenced several strains of Classical Swine Fever Virus (CSFV) by NGS on both Genome Sequencer FLX (GS FLX) and Iontorrent PGM platforms...

Design of Long Period Pseudo-Random Sequences from the Addition of m -Sequences over 𝔽 p

Directory of Open Access Journals (Sweden)

Ren Jian

2004-01-01

Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of m -sequences with pairwise-prime linear spans (AMPLS. Using m -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to 𝔽 2 , a signal set ( ( 2 n − 1 ( 2 m − 1 , ( 2 n + 1 ( 2 m + 1 , ( 2 ( n + 1 / 2 + 1 ( 2 ( m + 1 / 2 + 1 is constructed.

The Colliding Beams Sequencer

International Nuclear Information System (INIS)

Johnson, D.E.; Johnson, R.P.

1989-01-01

The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

Teaching Task Sequencing via Verbal Mediation.

Science.gov (United States)

Rusch, Frank R.; And Others

1987-01-01

Verbal sequence training was used to teach a moderately mentally retarded woman to sequence job-related tasks. Learning to say the tasks in the proper sequence resulted in the employee performing her tasks in that sequence, and the employee was capable of mediating her own work behavior when scheduled changes occurred. (Author/JDD)

RANDNA: a random DNA sequence generator.

Science.gov (United States)

Piva, Francesco; Principato, Giovanni

2006-01-01

Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length and the percentage of nucleotide composition. Sequences having the same nucleotide distribution of exonic, intronic or intergenic sequences can be generated. Its graphic interface makes it possible to easily set the parameters that characterize the sequences being produced and saved in a text format file. The pseudo-random number generator function of Borland Delphi 6 is used, since it guarantees a good randomness, a long cycle length and a high speed. We have checked the quality of sequences generated by the software, by means of well-known tests, both by themselves and versus genuine random sequences. We show the good quality of the generated sequences. The software, complete with examples and documentation, is freely available to users from: http://www.introni.it/en/software.

Dynamic Sequence Assignment.

Science.gov (United States)

1983-12-01

D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

General LTE Sequence

OpenAIRE

Billal, Masum

2015-01-01

In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

Gravity-Driven Deposits in an Active Margin (Ionian Sea) Over the Last 330,000 Years

Science.gov (United States)

Köng, Eléonore; Zaragosi, Sébastien; Schneider, Jean-Luc; Garlan, Thierry; Bachèlery, Patrick; Sabine, Marjolaine; San Pedro, Laurine

2017-11-01

In the Ionian Sea, the subduction of the Nubia plate underneath the Eurasia plate leads to an important sediment remobilization on the Calabrian Arc and the Mediterranean Ridge. These events are often associated with earthquakes and tsunamis. In this study, we analyze gravity-driven deposits in order to establish their recurrence time on the Calabrian Arc and the western Mediterranean Ridge. Four gravity cores collected on ridges and slope basins of accretionary prisms record turbidites, megaturbidites, slumping and micro-faults over the last 330,000 years. These turbidites were dated by correlation with a hemipelagic core with a multi-proxy approach: radiometric dating, δ18O, b* colour curve, sapropels and tephrochronology. The origin of the gravity-driven deposits was studied with a sedimentary approach: grain-size, lithology, thin section, geochemistry of volcanic glass. The results suggest three periods of presence/absence of gravity-driven deposits: a first on the western lobe of the Calabrian Arc between 330,000 and 250,000 years, a second between 120,000 years and present day on the eastern lobe of the Calabrian Arc and over the last 60,000 years on the western lobe, and a third on the Mediterranean Ridge over the last 37,000 years. Return times for gravity-driven deposits are around 1,000 years during the most important record periods. The turbidite activity also highlights the presence of volcaniclastic turbidites that seems to be link to the Etna changing morphology over the last 320,000 years.

Decidability of uniform recurrence of morphic sequences

OpenAIRE

Durand , Fabien

2012-01-01

We prove that the uniform recurrence of morphic sequences is decidable. For this we show that the number of derived sequences of uniformly recurrent morphic sequences is bounded. As a corollary we obtain that uniformly recurrent morphic sequences are primitive substitutive sequences.

Genomic sequencing of Pleistocene cave bears

Energy Technology Data Exchange (ETDEWEB)

Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

2005-04-01

Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

Targeted assembly of short sequence reads.

Directory of Open Access Journals (Sweden)

René L Warren

Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

Accurate Local-Ancestry Inference in Exome-Sequenced Admixed Individuals via Off-Target Sequence Reads

Science.gov (United States)

Hu, Youna; Willer, Cristen; Zhan, Xiaowei; Kang, Hyun Min; Abecasis, Gonçalo R.

2013-01-01

Estimates of the ancestry of specific chromosomal regions in admixed individuals are useful for studies of human evolutionary history and for genetic association studies. Previously, this ancestry inference relied on high-quality genotypes from genome-wide association study (GWAS) arrays. These high-quality genotypes are not always available when samples are exome sequenced, and exome sequencing is the strategy of choice for many ongoing genetic studies. Here we show that off-target reads generated during exome-sequencing experiments can be combined with on-target reads to accurately estimate the ancestry of each chromosomal segment in an admixed individual. To reconstruct local ancestry, our method SEQMIX models aligned bases directly instead of relying on hard genotype calls. We evaluate the accuracy of our method through simulations and analysis of samples sequenced by the 1000 Genomes Project and the NHLBI Grand Opportunity Exome Sequencing Project. In African Americans, we show that local-ancestry estimates derived by our method are very similar to those derived with Illumina’s Omni 2.5M genotyping array and much improved in relation to estimates that use only exome genotypes and ignore off-target sequencing reads. Software implementing this method, SEQMIX, can be applied to analysis of human population history or used for genetic association studies in admixed individuals. PMID:24210252

Method and apparatus for biological sequence comparison

Science.gov (United States)

Marr, T.G.; Chang, W.I.

1997-12-23

A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

Memory and learning with rapid audiovisual sequences

Science.gov (United States)

Keller, Arielle S.; Sekuler, Robert

2015-01-01

We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

The RNA world, automatic sequences and oncogenetics

Energy Technology Data Exchange (ETDEWEB)

Tahir Shah, K

1993-04-01

We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. (1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. (2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or ``accept`` other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs.

Memory and learning with rapid audiovisual sequences.

Science.gov (United States)

Keller, Arielle S; Sekuler, Robert

2015-01-01

We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed.

The RNA world, automatic sequences and oncogenetics

International Nuclear Information System (INIS)

Tahir Shah, K.

1993-04-01

We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. 1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. 2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or 'accept' other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs

Compressing DNA sequence databases with coil

Directory of Open Access Journals (Sweden)

Hendy Michael D

2008-05-01

Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

Region segmentation along image sequence

International Nuclear Information System (INIS)

Monchal, L.; Aubry, P.

1995-01-01

A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs

Phylogenetic Trees From Sequences

Science.gov (United States)

Ryvkin, Paul; Wang, Li-San

In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

Superposed orogenic collision and core-complex formation at the present contact between the Dinarides and the Pannonian basin: The Bukulja and Cer Mountains in central and western Serbia

Science.gov (United States)

Matenco, Liviu; Toljic, Marinko; Ducea, Mihai; Stojadinovic, Uros

2010-05-01

age and, in the case of Bukulja, with serpentinized ophiolites. The metamorphic sequences are generally characterized by a Paleozoic age meta-sedimentary basement and a meta-sedimentary and meta-volcanic sequence. In the case of Bukulja, a succession of contrasting metamorphosed lithologies has been observed such as sandstones, black limestones, shallow water white limestones, basic volcanic sequences, deep nodular limestones and turbiditic sequences. The lower part of the sequence represents a metamorphosed Triassic sequence similar to what has been defined as the Kopaonik and Studenica series in southern Serbia. This part of the sequence is characterized by at least 3 successive stages of folding, asymmetric folds with WSW-ward vergence and NNE-SSW upright folds being affected by vertical flattening folds associated with extension (see also Marovic et al., 2007). The upper part of the sequence, which is the only part outcropping along the eastern flank of the Cer granitoid, is made up by metamorphosed distal turbidites which have been palinologically dated in Bukulja as Upper Cretaceous in age. This is the metamorphosed equivalent of the Upper Cretaceous - Eocene "flysch"-type of deposits commonly observed elsewhere in the main Sava subduction zone. These rocks are overprinted with a pervasive and strong extensional milonitic foliation indicating top-100 movement of the hanging-wall and are in direct contact with non-metamorphosed, but similar Upper Cretaceous distal turbidites. This suggests a large-scale tectonic omission along the eastern flanks of the Bukulja and Cer detachment. In the case of Bukulja, the extension was associated with the formation of the Early Miocene Morava basin in the detachment hanging-wall, which is an endemic lacustrine precursor of the much larger Middle-Late Miocene Pannonian basin. These finding points towards a bi-modal evolution of the internal Dinarides in central and western Serbia near the present-day contact with the Pannonian

Mineralogía y génesis de la fracción fina de la serie de El Rinconcillo (formaciones Flysch del Campo de Gibraltar. SW de España

Directory of Open Access Journals (Sweden)

Carrasco, F.

1987-04-01

Full Text Available The stratigraphic sequence of El Rinconcillo belong to the Algeciras Unit. Illite, kaolinite, chlorite and interstratified illite-smectite are common minerals for materials of this Unit, but a high proportion of Fe-Al smectites and sporadic presence of palygorskite is characteristic of the series of El Rinconcillo in relation to the others studied in Northern Africa and Southwestern Spain. Illite, kaolinite and chlorite are considered to be inherited minerals. Smectides and interestratified illite-smectite are also inherited in the turbidites but they were formed in the source area by transformation from illite under different weathering degree. Finally, the formation of palygorskite in the Middle Eocene carbonatic turbidites accompanied by many smectide, and no kaolinite, is difficult to explain in relation with turbiditic materials. It is more feasible to suppose a removal process that implicates the existence of a previous clay sediment in which such association -palygorskite + smectite- took place by transformation and/or by neoformation.La serie de El Rinconcillo, atribuida a la Unidad de Algeciras, presenta variaciones mineralógicas notables respecto a las series "tipo" definidas en esta Unidad tanto en el norte de Africa como en el suroeste de España. Aunque en gran parte la mineralogía es común con otras series de esta Unidad (ilita, caolinita, clorita, interestratificados I-E, se diferencia no obstante, por la elevada proporción de esmectita Fe-Al y la presencia esporádica de paligorskita. Ilita, caolinta y clorita, se consideran minerales heredados. La esmectita y los interestratificados I-E son también heredados en las turbiditas, procedentes de la transformación de la ilita en el área fuente bajo diferente grado de meteorización. Finalmente, la formación de paligorskita en las turbidítas calcáreas del Eoceno medio acompañada por esmectita y la ausencia de caolinita en este tramo, es difícil de explicar en relación con

Fast and secure retrieval of DNA sequences

NARCIS (Netherlands)

2014-01-01

Sequence models are retrieved from a sequences index. The sequence models model DNA or RNA sequences stored in a database, and each comprises a finite memory tree source model and parameters for the finite memory tree source model. One or more DNA or RNA sequences stored in the database are

Robustness analysis of chiller sequencing control

International Nuclear Information System (INIS)

Liao, Yundan; Sun, Yongjun; Huang, Gongsheng

2015-01-01

Highlights: • Uncertainties with chiller sequencing control were systematically quantified. • Robustness of chiller sequencing control was systematically analyzed. • Different sequencing control strategies were sensitive to different uncertainties. • A numerical method was developed for easy selection of chiller sequencing control. - Abstract: Multiple-chiller plant is commonly employed in the heating, ventilating and air-conditioning system to increase operational feasibility and energy-efficiency under part load condition. In a multiple-chiller plant, chiller sequencing control plays a key role in achieving overall energy efficiency while not sacrifices the cooling sufficiency for indoor thermal comfort. Various sequencing control strategies have been developed and implemented in practice. Based on the observation that (i) uncertainty, which cannot be avoided in chiller sequencing control, has a significant impact on the control performance and may cause the control fail to achieve the expected control and/or energy performance; and (ii) in current literature few studies have systematically addressed this issue, this paper therefore presents a study on robustness analysis of chiller sequencing control in order to understand the robustness of various chiller sequencing control strategies under different types of uncertainty. Based on the robustness analysis, a simple and applicable method is developed to select the most robust control strategy for a given chiller plant in the presence of uncertainties, which will be verified using case studies

ABS: Sequence alignment by scanning

KAUST Repository

Bonny, Mohamed Talal; Salama, Khaled N.

2011-01-01

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.

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.

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.

Deciphering Depositional Signals in the Bed-Scale Stratigraphic Record of Submarine Channels

Science.gov (United States)

Sylvester, Z.; Covault, J. A.

2017-12-01

Submarine channels are important conduits of sediment transfer from rivers and shallow-marine settings into the deep sea. As such, the stratigraphic record of submarine-channel systems can store signals of past climate- and other environmental changes in their upstream sediment-source areas. This record is highly fragmented as channels are primarily locations of sediment bypass; channelized turbidity currents are likely to leave a more complete record in areas away from and above the thalweg. However, the link between the thick-bedded axial channel deposits that record a small number of flows and the much larger number of thin-bedded turbidites forming terrace- and levee deposits is poorly understood. We have developed a relatively simple two-dimensional model that, given a number of input flow parameters (mean velocity, grain size, duration of deposition, flow thickness), predicts the thickness and composition of the turbidite that is left behind in the channel and in the overbank areas. The model is based on a Rouse-type suspended sediment concentration profile and the Garcia-Parker entrainment function. In the vertical direction, turbidites tend to rapidly become thinner and finer-grained with height above thalweg, due to decreasing concentration. High near-thalweg concentrations result in thick axial beds. However, an increase in flow velocity can result in high entrainment and no deposition at the bottom of the channel, yet a thin layer of sand and mud is still deposited higher up on the channel bank. If channel thalwegs are largely in a bypass condition, relatively minor velocity fluctuations result in a few occasionally preserved thick beds in the axis, and numerous thin turbidites - and a more complete record - on the channel banks. We use near-seafloor data from the Niger Delta slope and an optimization algorithm to show how our model can be used to invert for likely flow parameters and match the bed thickness and grain size of 100 turbidites observed in a

Biosensors for DNA sequence detection

Science.gov (United States)

Vercoutere, Wenonah; Akeson, Mark

2002-01-01

DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

Transformed composite sequences for improved qubit addressing

Science.gov (United States)

Merrill, J. True; Doret, S. Charles; Vittorini, Grahame; Addison, J. P.; Brown, Kenneth R.

2014-10-01

Selective laser addressing of a single atom or atomic ion qubit can be improved using narrow-band composite pulse sequences. We describe a Lie-algebraic technique to generalize known narrow-band sequences and introduce sequences related by dilation and rotation of sequence generators. Our method improves known narrow-band sequences by decreasing both the pulse time and the residual error. Finally, we experimentally demonstrate these composite sequences using 40Ca+ ions trapped in a surface-electrode ion trap.

Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing.

Science.gov (United States)

Tan, M K

1991-08-01

A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup of the ancient supercontinent, Pangaea. These regions of the rRNA sequences have thus been conserved for at least 160 million years and are here compared with other eukaryotic, especially plant rRNAs.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

Directory of Open Access Journals (Sweden)

Jonas Binladen

2007-02-01

Full Text Available The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR reactions and subsequent sequencing runs have been unable to combine template DNA from multiple individuals, as homologous sequences cannot be subsequently assigned to their original sources.We use conventional PCR with 5'-nucleotide tagged primers to generate homologous DNA amplification products from multiple specimens, followed by sequencing through the high-throughput Genome Sequence 20 DNA Sequencing System (GS20, Roche/454 Life Sciences. Each DNA sequence is subsequently traced back to its individual source through 5'tag-analysis.We demonstrate that this new approach enables the assignment of virtually all the generated DNA sequences to the correct source once sequencing anomalies are accounted for (miss-assignment rate<0.4%. Therefore, the method enables accurate sequencing and assignment of homologous DNA sequences from multiple sources in single high-throughput GS20 run. We observe a bias in the distribution of the differently tagged primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution of the sequences as sorted by the second nucleotide of the dinucleotide tags. As the results are based on a single GS20 run, the general applicability of the approach requires confirmation. However, our experiments demonstrate that 5'primer tagging is a useful method in which the sequencing power of the GS20 can be applied to PCR-based assays of multiple homologous PCR products. The new approach will be of value to a broad range of research areas, such as those of comparative genomics, complete mitochondrial

Accident sequence quantification with KIRAP

Energy Technology Data Exchange (ETDEWEB)

Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong

1997-01-01

The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP`s cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs.

Accident sequence quantification with KIRAP

International Nuclear Information System (INIS)

Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

1997-01-01

The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

A measurement of disorder in binary sequences

Science.gov (United States)

Gong, Longyan; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

2015-03-01

We propose a complex quantity, AL, to characterize the degree of disorder of L-length binary symbolic sequences. As examples, we respectively apply it to typical random and deterministic sequences. One kind of random sequences is generated from a periodic binary sequence and the other is generated from the logistic map. The deterministic sequences are the Fibonacci and Thue-Morse sequences. In these analyzed sequences, we find that the modulus of AL, denoted by |AL | , is a (statistically) equivalent quantity to the Boltzmann entropy, the metric entropy, the conditional block entropy and/or other quantities, so it is a useful quantitative measure of disorder. It can be as a fruitful index to discern which sequence is more disordered. Moreover, there is one and only one value of |AL | for the overall disorder characteristics. It needs extremely low computational costs. It can be easily experimentally realized. From all these mentioned, we believe that the proposed measure of disorder is a valuable complement to existing ones in symbolic sequences.

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Directory of Open Access Journals (Sweden)

Jason D Thompson

Full Text Available Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

Science.gov (United States)

Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, Andre

2012-01-01

Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

Static multiplicities in heterogeneous azeotropic distillation sequences

DEFF Research Database (Denmark)

Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

1998-01-01

In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

Sedimentation in a Submarine Seamount Apron at Site U1431, International Ocean Discovery Program Expedition 349, South China Sea

Science.gov (United States)

Dadd, K. A.; Clift, P. D.; Hyun, S.; Jiang, T.; Liu, Z.

2014-12-01

International Ocean Discovery Program (IODP) Expedition 349 Site U1431 is located near the relict spreading ridge in the East Subbasin of the South China Sea. Holes at this site were drilled close to seamounts and intersected the volcaniclastic apron. Volcaniclastic breccia and sandstone at Site U1431 are dated as late middle Miocene to early late Miocene (~8-13 Ma), suggesting a 5 m.y. duration of seamount volcanism. The apron is approximately 200 m thick and is sandwiched between non-volcaniclastic units that represent the background sedimentation. These comprise dark greenish gray clay, silt, and nannofossil ooze interpreted as turbidite and hemipelagic deposits that accumulated at abyssal water depths. At its base, the seamount sequence begins with dark greenish gray sandstone, siltstone, and claystone in upward fining sequences interpreted as turbidites intercalated with minor intervals of volcaniclastic breccia. Upsection the number and thickness of breccia layers increases with some beds up to 4.8 m and possibly 14.5 m thick. The breccia is typically massive, ungraded, and poorly sorted with angular to subangular basaltic clasts, as well as minor reworked subrounded calcareous mudstone, mudstone, and sandstone clasts. Basaltic clasts include nonvesicular aphyric basalt, sparsely vesicular aphyric basalt, highly vesicular aphyric basalt, and nonvesicular glassy basalt. Mudstone clasts are clay rich and contain foraminifer fossils. The matrix comprises up to 40% of the breccia beds and is a mix of clay, finer grained altered basalt clasts, and mafic vitroclasts with rare foraminifer fossils. Some layers have calcite cement between clasts. Volcaniclastic sandstone and claystone cycles interbedded with the breccia layers have current ripples and parallel laminations indicative of high-energy flow conditions during sedimentation. The breccia beds were most likely deposited as a series of debris flows or grain flows. This interpretation is supported by their

Permutation Entropy for Random Binary Sequences

Directory of Open Access Journals (Sweden)

Lingfeng Liu

2015-12-01

Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

Perfect sequences over the real quaternions

OpenAIRE

Kuznetsov, Oleg

2017-01-01

In this Thesis, perfect sequences over the real quaternions are first considered. Definitions for the right and left periodic autocorrelation functions are given, and right and left perfect sequences introduced. It is shown that the right (left) perfection of any sequence implies the left (right) perfection, so concepts of right and left perfect sequences over the real quaternions are equivalent. Unitary transformations of the quaternion space ℍ are then considered. Using the equivalence of t...

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.

Science.gov (United States)

Schirmer, Melanie; Ijaz, Umer Z; D'Amore, Rosalinda; Hall, Neil; Sloan, William T; Quince, Christopher

2015-03-31

With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molecular diagnostics. However, Illumina error profiles are still poorly understood and programs are therefore not designed for the idiosyncrasies of Illumina data. A better knowledge of the error patterns is essential for sequence analysis and vital if we are to draw valid conclusions. Studying true genetic variation in a population sample is fundamental for understanding diseases, evolution and origin. We conducted a large study on the error patterns for the MiSeq based on 16S rRNA amplicon sequencing data. We tested state-of-the-art library preparation methods for amplicon sequencing and showed that the library preparation method and the choice of primers are the most significant sources of bias and cause distinct error patterns. Furthermore we tested the efficiency of various error correction strategies and identified quality trimming (Sickle) combined with error correction (BayesHammer) followed by read overlapping (PANDAseq) as the most successful approach, reducing substitution error rates on average by 93%. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Sequences for Student Investigation

Science.gov (United States)

Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

2004-01-01

We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

Image sequence analysis

CERN Document Server

1981-01-01

The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

SAAS: Short Amino Acid Sequence - A Promising Protein Secondary Structure Prediction Method of Single Sequence

Directory of Open Access Journals (Sweden)

Zhou Yuan Wu

2013-07-01

Full Text Available In statistical methods of predicting protein secondary structure, many researchers focus on single amino acid frequencies in α-helices, β-sheets, and so on, or the impact near amino acids on an amino acid forming a secondary structure. But the paper considers a short sequence of amino acids (3, 4, 5 or 6 amino acids as integer, and statistics short sequence's probability forming secondary structure. Also, many researchers select low homologous sequences as statistical database. But this paper select whole PDB database. In this paper we propose a strategy to predict protein secondary structure using simple statistical method. Numerical computation shows that, short amino acids sequence as integer to statistics, which can easy see trend of short sequence forming secondary structure, and it will work well to select large statistical database (whole PDB database without considering homologous, and Q3 accuracy is ca. 74% using this paper proposed simple statistical method, but accuracy of others statistical methods is less than 70%.

Transcriptome sequencing of the Microarray Quality Control (MAQC RNA reference samples using next generation sequencing

Directory of Open Access Journals (Sweden)

Thierry-Mieg Danielle

2009-06-01

Full Text Available Abstract Background Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC reference RNA samples using Roche's 454 Genome Sequencer FLX. Results We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database. Conclusion Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.

Comparative genomics beyond sequence-based alignments

DEFF Research Database (Denmark)

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

2008-01-01

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

ASAP: Amplification, sequencing & annotation of plastomes

Directory of Open Access Journals (Sweden)

Folta Kevin M

2005-12-01

Full Text Available Abstract Background Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate ~1 – 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera. Results 100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

DEFF Research Database (Denmark)

Binladen, Jonas; Gilbert, M Thomas P; Bollback, Jonathan P

2007-01-01

BACKGROUND: The invention of the Genome Sequence 20 DNA Sequencing System (454 parallel sequencing platform) has enabled the rapid and high-volume production of sequence data. Until now, however, individual emulsion PCR (emPCR) reactions and subsequent sequencing runs have been unable to combine...... primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution...

cDNA sequence quality data - Budding yeast cDNA sequencing project | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us Budding yeast cDNA sequencing project cDNA sequence quality data Data detail Data name cDNA sequence quality... data DOI 10.18908/lsdba.nbdc00838-003 Description of data contents Phred's quality score. P...tion Download License Update History of This Database Site Policy | Contact Us cDNA sequence quality

Spreading Sequences Generated Using Asymmetrical Integer-Number Maps

Directory of Open Access Journals (Sweden)

V. Sebesta

2007-09-01

Full Text Available Chaotic sequences produced by piecewise linear maps can be transformed to binary sequences. The binary sequences are optimal for the asynchronous DS/CDMA systems in case of certain shapes of the maps. This paper is devoted to the one-to-one integer-number maps derived from the suitable asymmetrical piecewise linear maps. Such maps give periodic integer-number sequences, which can be transformed to the binary sequences. The binary sequences produced via proposed modified integer-number maps are perfectly balanced and embody good autocorrelation and crosscorrelation properties. The number of different binary sequences is sizable. The sequences are suitable as spreading sequences in DS/CDMA systems.

Genomic sequencing in clinical trials

OpenAIRE

Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

2011-01-01

Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

Sedimentology of middle ordovician carbonates in the Argentine precordillera: evidence of regional relative sea-level changes

Science.gov (United States)

Keller, M.; Eberlein, S.; Lehnert, O.

1993-07-01

The Las Aguaditas Formation in the Argentine Precordillera of San Juan is the only Ordovician carbonate sequence deposited on a slope. Spiculites, mudstones and calcisiltites represent the autochthonous sediments, characterized by a fine lamination, rare fossils and their dark colour. The pelagic fauna consists of rare radiolarians/calcispheres, trinucleid trilobites, graptolites and conodonts. The latter are typical of an open marine environment and proved a Llanvirn—Llandeilo age for the Las Aguaditas Formation. In the upper part of the succession there are several intercalations of megabreccias. Their thickness decreases from about 20 to 4 m towards the top of the formation, accompanied by an increasing amount of carbonate turbidites. The clasts of the breccias are derived from the slope as well as the platform. Each of the megabreccia horizons represents a system of channels, lobes and interchannel deposits, which together form a slope apron. On top of the lower breccia a small biostrome developed, where bryozoans and crinoids are preserved in an autochthonous position. Sedimentation of the Las Aguaditas Formation started with the drowning of the underlying carbonate platform (San Juan limestones). Near the Arenig-Llanvirn boundary, a rapid ecstatic sea-level rise led to the deposition of graptolitic black shales and mudstones. Upwards, allochthonous carbonates become increasingly abundant. The onset of megabreccia deposition coincides with a major relative sea-level fall, caused by block movements in connection with rifting. The subsequent transition from breccia formation towards turbiditic sedimentation corresponds to an environmental shift from the slope towards the toe of slope and basin and marks a renewed moderate sea-level rise.

Compact flow diagrams for state sequences

NARCIS (Netherlands)

Buchin, K.A.; Buchin, M.E.; Gudmundsson, J.; Horton, M.J.; Sijben, S.

2016-01-01

We introduce the concept of compactly representing a large number of state sequences, e.g., sequences of activities, as a flow diagram. We argue that the flow diagram representation gives an intuitive summary that allows the user to detect patterns among large sets of state sequences. Simplified,

The presence of five nifH-like sequences in Clostridium pasteurianum: sequence divergence and transcription properties.

OpenAIRE

Wang, S Z; Chen, J S; Johnson, J L

1988-01-01

The nifH gene encodes the iron protein (component II) of the nitrogenase complex. We have previously shown the presence in Clostridium pasteurianum of two nifH-like sequences in addition to the nifH1 gene which codes for a protein identical to the isolated iron protein. In the present study, we report that there are at least five nifH-like sequences in C. pasteurianum. DNA sequencing data indicate that the six nifH (nifH1) and nifH-like (nifH2, nifH3, nifH4, nifH5 and nifH6) sequences are not...

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

Directory of Open Access Journals (Sweden)

Takeru Nakazato

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

Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis

DEFF Research Database (Denmark)

Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta

2014-01-01

The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease...... digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72...... individuals using only 24 barcoded libraries....

Comparative analysis of sequences from PT 2013

DEFF Research Database (Denmark)

Mikkelsen, Susie Sommer

Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...... diseases in Europe. As part of the EURL proficiency test for fish diseases it is required to sequence any RANA virus isolates found in any of the samples. It is also highly recommended to sequence the ISA virus to determine whether it be HPRΔ or HPR0. Furthermore, it is recommended that any VHSV and IHNV...... isolates be genotyped. As part of the evaluation of the proficiency results it was decided this year to look into the quality and similarity of the sequence results for selected viruses. Ampoule III in the proficiency test 2013 contained an EHNV isolate. The EURL received 43 sequences from 41 laboratories...

Superquakes and Supercycles

Science.gov (United States)

Goldfinger, C.; Ikeda, Y.; Yeats, R. S.

2011-12-01

The recent Mw=9 superquake off Tohoku Japan, and the 2004 Sumatra-Andaman superquake have humbled many in earthquake research. Neither region was thought capable of earthquakes of magnitudes exceeding Mw~8.4 based on historical records and theories based on short instrumental records. In NE Japan, horizontal shortening is ~5-7 mm/yr. based on faulting and regional uplift data. On the Pacific coast, high rates of subsidence from tide gauges, and geodetic observations revealed E-W contraction at several tens of mm/yr. Only a fraction (AD 1920) than the intervening events which averaged 1.5-2 m. In Cascadia, a 10ka paleoseismic record includes evidence of segmented ruptures, clustering, and several outsized events. Goldfinger et al. (2011) compared the mass of correlated turbidite deposits along strike, and found strong correlation between disparate sites. They conclude the earthquake magnitude and turbidite mass are related for many of the Cascadia events. The two outsized events, dated at ~ 5960 and 8810 yrs. BP, consistently have two to five times the average turbidite mass for Holocene events at many sites. To examine long term cycling of kinetic energy, we scale turbidite mass (energy release) to balance plate convergence (energy gain) to generate a 10ka energy time series for Cascadia. A robust pattern is observed, and includes long term increases and declines in stored "energy state" which we term "supercycles". If Cascadia is representative, this suggests that recurrence models may be neither time nor slip predictable and cannot be based on short instrumental records.

Next-generation sequencing

DEFF Research Database (Denmark)

Rieneck, Klaus; Bak, Mads; Jønson, Lars

2013-01-01

, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

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

DEFF Research Database (Denmark)

Alquezar-Planas, David E; Fordyce, Sarah Louise

2012-01-01

Since the development of so-called "next generation" high-throughput sequencing in 2005, this technology has been applied to a variety of fields. Such applications include disease studies, evolutionary investigations, and ancient DNA. Each application requires a specialized protocol to ensure...... that the data produced is optimal. Although much of the procedure can be followed directly from the manufacturer's protocols, the key differences lie in the library preparation steps. This chapter presents an optimized protocol for the sequencing of fossil remains and museum specimens, commonly referred...

EGNAS: an exhaustive DNA sequence design algorithm

Directory of Open Access Journals (Sweden)

Kick Alfred

2012-06-01

Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

Integrated sequence analysis. Final report

International Nuclear Information System (INIS)

Andersson, K.; Pyy, P.

1998-02-01

The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

Integrated sequence analysis. Final report

Energy Technology Data Exchange (ETDEWEB)

Andersson, K.; Pyy, P

1998-02-01

The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

Sequence protein identification by randomized sequence database and transcriptome mass spectrometry (SPIDER-TMS): from manual to automatic application of a 'de novo sequencing' approach.

Science.gov (United States)

Pascale, Raffaella; Grossi, Gerarda; Cruciani, Gabriele; Mecca, Giansalvatore; Santoro, Donatello; Sarli Calace, Renzo; Falabella, Patrizia; Bianco, Giuliana

Sequence protein identification by a randomized sequence database and transcriptome mass spectrometry software package has been developed at the University of Basilicata in Potenza (Italy) and designed to facilitate the determination of the amino acid sequence of a peptide as well as an unequivocal identification of proteins in a high-throughput manner with enormous advantages of time, economical resource and expertise. The software package is a valid tool for the automation of a de novo sequencing approach, overcoming the main limits and a versatile platform useful in the proteomic field for an unequivocal identification of proteins, starting from tandem mass spectrometry data. The strength of this software is that it is a user-friendly and non-statistical approach, so protein identification can be considered unambiguous.

Fast global sequence alignment technique

KAUST Repository

Bonny, Mohamed Talal; Salama, Khaled N.

2011-01-01

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

Ancestral sequence alignment under optimal conditions

Directory of Open Access Journals (Sweden)

Brown Daniel G

2005-11-01

Full Text Available Abstract Background Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms. An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree. In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences. Results We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth. We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang. Conclusion We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the

Recursive sequences in first-year calculus

Science.gov (United States)

Krainer, Thomas

2016-02-01

This article provides ready-to-use supplementary material on recursive sequences for a second-semester calculus class. It equips first-year calculus students with a basic methodical procedure based on which they can conduct a rigorous convergence or divergence analysis of many simple recursive sequences on their own without the need to invoke inductive arguments as is typically required in calculus textbooks. The sequences that are accessible to this kind of analysis are predominantly (eventually) monotonic, but also certain recursive sequences that alternate around their limit point as they converge can be considered.

Hardware Accelerated Sequence Alignment with Traceback

Directory of Open Access Journals (Sweden)

Scott Lloyd

2009-01-01

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 presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

Transcription blockage by homopurine DNA sequences: role of sequence composition and single-strand breaks

Science.gov (United States)

Belotserkovskii, Boris P.; Neil, Alexander J.; Saleh, Syed Shayon; Shin, Jane Hae Soo; Mirkin, Sergei M.; Hanawalt, Philip C.

2013-01-01

The ability of DNA to adopt non-canonical structures can affect transcription and has broad implications for genome functioning. We have recently reported that guanine-rich (G-rich) homopurine-homopyrimidine sequences cause significant blockage of transcription in vitro in a strictly orientation-dependent manner: when the G-rich strand serves as the non-template strand [Belotserkovskii et al. (2010) Mechanisms and implications of transcription blockage by guanine-rich DNA sequences., Proc. Natl Acad. Sci. USA, 107, 12816–12821]. We have now systematically studied the effect of the sequence composition and single-stranded breaks on this blockage. Although substitution of guanine by any other base reduced the blockage, cytosine and thymine reduced the blockage more significantly than adenine substitutions, affirming the importance of both G-richness and the homopurine-homopyrimidine character of the sequence for this effect. A single-strand break in the non-template strand adjacent to the G-rich stretch dramatically increased the blockage. Breaks in the non-template strand result in much weaker blockage signals extending downstream from the break even in the absence of the G-rich stretch. Our combined data support the notion that transcription blockage at homopurine-homopyrimidine sequences is caused by R-loop formation. PMID:23275544

SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.

Science.gov (United States)

Wala, Jeremiah; Beroukhim, Rameen

2017-03-01

We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. jwala@broadinstitue.org ; rameen@broadinstitute.org. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Exploration of noncoding sequences in metagenomes.

Directory of Open Access Journals (Sweden)

Fabián Tobar-Tosse

Full Text Available Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C content, Codon Usage (Cd, Trinucleotide Usage (Tn, and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment.

Sequence-to-Sequence Prediction of Vehicle Trajectory via LSTM Encoder-Decoder Architecture

OpenAIRE

Park, Seong Hyeon; Kim, ByeongDo; Kang, Chang Mook; Chung, Chung Choo; Choi, Jun Won

2018-01-01

In this paper, we propose a deep learning based vehicle trajectory prediction technique which can generate the future trajectory sequence of surrounding vehicles in real time. We employ the encoder-decoder architecture which analyzes the pattern underlying in the past trajectory using the long short-term memory (LSTM) based encoder and generates the future trajectory sequence using the LSTM based decoder. This structure produces the $K$ most likely trajectory candidates over occupancy grid ma...

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

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Graner Andreas

2008-10-01

Full Text Available Abstract Background Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR index can be generated to map repetitive regions in genomic sequences. Results We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised. Conclusion An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences regions in uncharacterised genomic sequences. The restriction that a particular

Third-Generation Sequencing and Analysis of Four Complete Pig Liver Esterase Gene Sequences in Clones Identified by Screening BAC Library.

Science.gov (United States)

Zhou, Qiongqiong; Sun, Wenjuan; Liu, Xiyan; Wang, Xiliang; Xiao, Yuncai; Bi, Dingren; Yin, Jingdong; Shi, Deshi

2016-01-01

Pig liver carboxylesterase (PLE) gene sequences in GenBank are incomplete, which has led to difficulties in studying the genetic structure and regulation mechanisms of gene expression of PLE family genes. The aim of this study was to obtain and analysis of complete gene sequences of PLE family by screening from a Rongchang pig BAC library and third-generation PacBio gene sequencing. After a number of existing incomplete PLE isoform gene sequences were analysed, primers were designed based on conserved regions in PLE exons, and the whole pig genome used as a template for Polymerase chain reaction (PCR) amplification. Specific primers were then selected based on the PCR amplification results. A three-step PCR screening method was used to identify PLE-positive clones by screening a Rongchang pig BAC library and PacBio third-generation sequencing was performed. BLAST comparisons and other bioinformatics methods were applied for sequence analysis. Five PLE-positive BAC clones, designated BAC-10, BAC-70, BAC-75, BAC-119 and BAC-206, were identified. Sequence analysis yielded the complete sequences of four PLE genes, PLE1, PLE-B9, PLE-C4, and PLE-G2. Complete PLE gene sequences were defined as those containing regulatory sequences, exons, and introns. It was found that, not only did the PLE exon sequences of the four genes show a high degree of homology, but also that the intron sequences were highly similar. Additionally, the regulatory region of the genes contained two 720bps reverse complement sequences that may have an important function in the regulation of PLE gene expression. This is the first report to confirm the complete sequences of four PLE genes. In addition, the study demonstrates that each PLE isoform is encoded by a single gene and that the various genes exhibit a high degree of sequence homology, suggesting that the PLE family evolved from a single ancestral gene. Obtaining the complete sequences of these PLE genes provides the necessary foundation for

Exome sequencing and genetic testing for MODY.

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Stefan Johansson

Full Text Available Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive.The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results.We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism.On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0-4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively, thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes.Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.

FRESCO: Referential compression of highly similar sequences.

Science.gov (United States)

Wandelt, Sebastian; Leser, Ulf

2013-01-01

In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

Genome Sequence of Australian Indigenous Wine Yeast Torulaspora delbrueckii COFT1 Using Nanopore Sequencing.

Science.gov (United States)

Tondini, Federico; Jiranek, Vladimir; Grbin, Paul R; Onetto, Cristobal A

2018-04-26

Here, we report the first sequenced genome of an indigenous Australian wine isolate of Torulaspora delbrueckii using the Oxford Nanopore MinION and Illumina HiSeq sequencing platforms. The genome size is 9.4 Mb and contains 4,831 genes. Copyright © 2018 Tondini et al.

Targeted Gene Sequencing and Whole-Exome Sequencing in Autopsied Fetuses with Prenatally Diagnosed Kidney Anomalies

DEFF Research Database (Denmark)

Rasmussen, M; Sunde, L; Nielsen, M L

2018-01-01

Identification of fetal kidney anomalies invites questions about underlying causes and recurrence risk in future pregnancies. We therefore investigated the diagnostic yield of next-generation sequencing in fetuses with bilateral kidney anomalies and the correlation between disrupted genes and fetal...... phenotypes. Fetuses with bilateral kidney anomalies were screened using an in-house-designed kidney-gene panel. In families where candidate variants were not identified, whole-exome sequencing was performed. Genes uncovered by this analysis were added to our kidney-panel. We identified likely deleterious...... of nephronophthisis. Exome sequencing identified ROBO1 variants in one family and a GREB1L variant in another family. GREB1L and ROBO1 were added to our kidney-gene panel and additional variants were identified. Next-generation sequencing substantially contributes to identifying causes of fetal kidney anomalies...

Sequence Factorization with Multiple References.

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Sebastian Wandelt

Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

Multiplexed microsatellite recovery using massively parallel sequencing

Science.gov (United States)

Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

2011-01-01

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

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Li Kelvin

2012-11-01

Full Text Available Abstract Background In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. Results We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute’s (JCVI high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Conclusions Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus

Sequence analysis of Leukemia DNA

Science.gov (United States)

Nacong, Nasria; Lusiyanti, Desy; Irawan, Muhammad. Isa

2018-03-01

Cancer is a very deadly disease, one of which is leukemia disease or better known as blood cancer. The cancer cell can be detected by taking DNA in laboratory test. This study focused on local alignment of leukemia and non leukemia data resulting from NCBI in the form of DNA sequences by using Smith-Waterman algorithm. SmithWaterman algorithm was invented by TF Smith and MS Waterman in 1981. These algorithms try to find as much as possible similarity of a pair of sequences, by giving a negative value to the unequal base pair (mismatch), and positive values on the same base pair (match). So that will obtain the maximum positive value as the end of the alignment, and the minimum value as the initial alignment. This study will use sequences of leukemia and 3 sequences of non leukemia.

Locomotor sequence learning in visually guided walking

DEFF Research Database (Denmark)

Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

2016-01-01

walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 years, N = 20) could learn a specific sequence...... of step lengths over 300 training steps. Younger children (age 6-10 years, N = 8) have lower baseline performance, but their magnitude and rate of sequence learning was the same compared to older children (11-16 years, N = 10) and healthy adults. In addition, learning capacity may be more limited...... to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence non-specific learning during...

Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences.

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Alexander M Sevy

2015-07-01

Full Text Available Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a 'single state' design (SSD paradigm. Multi-specificity design (MSD, on the other hand, involves considering the stability of multiple protein states simultaneously. We have developed a novel MSD algorithm, which we refer to as REstrained CONvergence in multi-specificity design (RECON. The algorithm allows each state to adopt its own sequence throughout the design process rather than enforcing a single sequence on all states. Convergence to a single sequence is encouraged through an incrementally increasing convergence restraint for corresponding positions. Compared to MSD algorithms that enforce (constrain an identical sequence on all states the energy landscape is simplified, which accelerates the search drastically. As a result, RECON can readily be used in simulations with a flexible protein backbone. We have benchmarked RECON on two design tasks. First, we designed antibodies derived from a common germline gene against their diverse targets to assess recovery of the germline, polyspecific sequence. Second, we design "promiscuous", polyspecific proteins against all binding partners and measure recovery of the native sequence. We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes.

Quantitative comparison between a multiecho sequence and a single-echo sequence for susceptibility-weighted phase imaging.

Science.gov (United States)

Gilbert, Guillaume; Savard, Geneviève; Bard, Céline; Beaudoin, Gilles

2012-06-01

The aim of this study was to investigate the benefits arising from the use of a multiecho sequence for susceptibility-weighted phase imaging using a quantitative comparison with a standard single-echo acquisition. Four healthy adult volunteers were imaged on a clinical 3-T system using a protocol comprising two different three-dimensional susceptibility-weighted gradient-echo sequences: a standard single-echo sequence and a multiecho sequence. Both sequences were repeated twice in order to evaluate the local noise contribution by a subtraction of the two acquisitions. For the multiecho sequence, the phase information from each echo was independently unwrapped, and the background field contribution was removed using either homodyne filtering or the projection onto dipole fields method. The phase information from all echoes was then combined using a weighted linear regression. R2 maps were also calculated from the multiecho acquisitions. The noise standard deviation in the reconstructed phase images was evaluated for six manually segmented regions of interest (frontal white matter, posterior white matter, globus pallidus, putamen, caudate nucleus and lateral ventricle). The use of the multiecho sequence for susceptibility-weighted phase imaging led to a reduction of the noise standard deviation for all subjects and all regions of interest investigated in comparison to the reference single-echo acquisition. On average, the noise reduction ranged from 18.4% for the globus pallidus to 47.9% for the lateral ventricle. In addition, the amount of noise reduction was found to be strongly inversely correlated to the estimated R2 value (R=-0.92). In conclusion, the use of a multiecho sequence is an effective way to decrease the noise contribution in susceptibility-weighted phase images, while preserving both contrast and acquisition time. The proposed approach additionally permits the calculation of R2 maps. Copyright © 2012 Elsevier Inc. All rights reserved.

Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data.

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Manal Helal

Full Text Available BACKGROUND: The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 sequences of 16S rRNA gene with a defined species in GenBank, and 110 sequences of 16S rRNA gene with no defined species, all within the genus Nocardia. METHODS: A total of 364 16S rRNA gene sequences of Nocardia species were studied. In addition, 110 16S rRNA gene sequences assigned only to the Nocardia genus level at the time of submission to GenBank were used for machine learning classification experiments. Different clustering algorithms were compared with a novel algorithm or the linear mapping (LM of the distance matrix. Principal Components Analysis was used for the dimensionality reduction and visualization. RESULTS: The LM algorithm achieved the highest performance and classified the set of 364 16S rRNA sequences into 80 clusters, the majority of which (83.52% corresponded with the original species. The most representative 16S rRNA sequences for individual Nocardia species have been identified as 'centroids' in respective clusters from which the distances to all other sequences were minimized; 110 16S rRNA gene sequences with identifications recorded only at the genus level were classified using machine learning methods. Simple kNN machine learning demonstrated the highest performance and classified Nocardia species sequences with an accuracy of 92.7% and a mean frequency of 0.578. CONCLUSION: The identification of centroids of 16S rRNA gene sequence clusters using novel distance matrix clustering enables the identification of the most representative sequences for each individual species of Nocardia and allows the quantitation of inter- and intra

Farey sequences and resistor networks

Indian Academy of Sciences (India)

Green's function, while the perturbation of a network is investigated in [3]. ... In Theorem 1 below, we employ the Farey sequence to establish a strict .... We next show that the Farey sequence method is applicable for circuits with n or fewer.

The Biomolecule Sequencer Project: Nanopore Sequencing as a Dual-Use Tool for Crew Health and Astrobiology Investigations

Science.gov (United States)

John, K. K.; Botkin, D. S.; Burton, A. S.; Castro-Wallace, S. L.; Chaput, J. D.; Dworkin, J. P.; Lehman, N.; Lupisella, M. L.; Mason, C. E.; Smith, D. J.;

mirVAFC: A Web Server for Prioritizations of Pathogenic Sequence Variants from Exome Sequencing Data via Classifications.

Science.gov (United States)

Li, Zhongshan; Liu, Zhenwei; Jiang, Yi; Chen, Denghui; Ran, Xia; Sun, Zhong Sheng; Wu, Jinyu

2017-01-01

Exome sequencing has been widely used to identify the genetic variants underlying human genetic disorders for clinical diagnoses, but the identification of pathogenic sequence variants among the huge amounts of benign ones is complicated and challenging. Here, we describe a new Web server named mirVAFC for pathogenic sequence variants prioritizations from clinical exome sequencing (CES) variant data of single individual or family. The mirVAFC is able to comprehensively annotate sequence variants, filter out most irrelevant variants using custom criteria, classify variants into different categories as for estimated pathogenicity, and lastly provide pathogenic variants prioritizations based on classifications and mutation effects. Case studies using different types of datasets for different diseases from publication and our in-house data have revealed that mirVAFC can efficiently identify the right pathogenic candidates as in original work in each case. Overall, the Web server mirVAFC is specifically developed for pathogenic sequence variant identifications from family-based CES variants using classification-based prioritizations. The mirVAFC Web server is freely accessible at https://www.wzgenomics.cn/mirVAFC/. © 2016 WILEY PERIODICALS, INC.

Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

Science.gov (United States)

Leaché, Adam D.; Chavez, Andreas S.; Jones, Leonard N.; Grummer, Jared A.; Gottscho, Andrew D.; Linkem, Charles W.

2015-01-01

Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both “recent” and “deep” timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus. PMID:25663487

Application of Quaternion in improving the quality of global sequence alignment scores for an ambiguous sequence target in Streptococcus pneumoniae DNA

Science.gov (United States)

Lestari, D.; Bustamam, A.; Novianti, T.; Ardaneswari, G.

2017-07-01

DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (PA, PT, PG, PC), where PA, PT, PG, PC are the probability of A, T, G, C bases that could appear in Q and PA + PT + PG + PC = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

Diagnostic accuracy of unenhanced, contrast-enhanced perfusion and angiographic MRI sequences for pulmonary embolism diagnosis: results of independent sequence readings

Energy Technology Data Exchange (ETDEWEB)

Revel, Marie Pierre [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Hotel-Dieu, Service de Radiologie, Paris (France); Sanchez, Olivier; Meyer, Guy [Hopital Europeen Georges Pompidou, APHP, Respiratory and intensive care and, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM Unite 765, Paris (France); Lefort, Catherine; Couchon, Sophie; Hernigou, Anne; Frija, Guy [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Niarra, Ralph [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Chatellier, Gilles [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM CIC-EC E4, Paris (France)

2013-09-15

To independently evaluate unenhanced, contrast-enhanced perfusion and angiographic MR sequences for pulmonary embolism (PE) diagnosis. Prospective investigation, including 274 patients who underwent perfusion, unenhanced 2D steady-state-free-precession (SSFP) and contrast-enhanced 3D angiographic MR sequences on a 1.5-T unit, in addition to CTA (CT angiography). Two independent readers evaluated each sequence independently in random order. Sensitivity, specificity, predictive values and inter-reader agreement were calculated for each sequence, excluding sequences judged inconclusive. Sensitivity was also calculated according to PE location. Contrast-enhanced angiographic sequences showed the highest sensitivity (82.9 and 89.7 %, reader 1 and reader 2, respectively), specificity (98.5 and 100 %) and agreement (kappa value 0.77). Unenhanced angiographic sequences, although less sensitive overall (68.7 and 76.4 %), were sensitive for the detection of proximal PE (92.7 and 100 %) and showed high specificity (96.1 and 99.1 %) and good agreement (kappa value 0.62). Perfusion sequences showed lower sensitivity (75.0 and 79.3 %), specificity (84.8 and 89.7 %) and agreement (kappa value 0.51), and a negative predictive value of 84.8 % at best. Compared with contrast-enhanced angiographic sequences, unenhanced sequences demonstrate lower sensitivity, except for proximal PE, but high specificity and agreement. The negative predictive value of perfusion sequences was insufficient to safely rule out PE. (orig.)

Lithology and surficial sediment distribution: northern Hatteras Abyssal Plain

International Nuclear Information System (INIS)

Dickson, S.M.; Laine, E.P.; Friedrich, N.E.

1985-01-01

Surficial sediments of the LLWODP study area E-N3 have several common characteristics and a few anomalous features. All of the 26 surficial samples examined are Holocene in age. In E-N3, the Holocene sequence ranges from 12-90 cm. The sequence is composed primarily of brown foraminiferal lutite. The lutites show evidence of burrowing by benthic animals in the form of burrows infilled with sediment of a different color. Below the bioturbated lutites is a dark brown, iron-enriched horizon stratigraphically near (within a few centimeters of) the Pleistocene/Holocene boundary. The vertical extent of this unit, which ranges from 2-22 cm, varies systematically within the study area. The maximum thickness is found in a region most removed from the terrigenous sediment entry points. Fine-grained turbidity currents, an abyssal current, and a debris flow created the uncommon features of the surficial sediments. The areal extent of these deposits is estimated as 10% of the E-N3 region below 5300 m. The largest turbidite is probably greater than 2000 km 2 in extent. However, evidence of coarse-grained turbidity current activity in the Holocene is absent. Hemipelagic deposition during the Holocene has resulted in a texturally uniform sequence of surficial sediments. 22 references, 10 figures, 6 tables

Enhanced throughput for infrared automated DNA sequencing

Science.gov (United States)

Middendorf, Lyle R.; Gartside, Bill O.; Humphrey, Pat G.; Roemer, Stephen C.; Sorensen, David R.; Steffens, David L.; Sutter, Scott L.

1995-04-01

Several enhancements have been developed and applied to infrared automated DNA sequencing resulting in significantly higher throughput. A 41 cm sequencing gel (31 cm well- to-read distance) combines high resolution of DNA sequencing fragments with optimized run times yielding two runs per day of 500 bases per sample. A 66 cm sequencing gel (56 cm well-to-read distance) produces sequence read lengths of up to 1000 bases for ds and ss templates using either T7 polymerase or cycle-sequencing protocols. Using a multichannel syringe to load 64 lanes allows 16 samples (compatible with 96-well format) to be visualized for each run. The 41 cm gel configuration allows 16,000 bases per day (16 samples X 500 bases/sample X 2 ten hour runs/day) to be sequenced with the advantages of infrared technology. Enhancements to internal labeling techniques using an infrared-labeled dATP molecule (Boehringer Mannheim GmbH, Penzberg, Germany; Sequenase (U.S. Biochemical) have also been made. The inclusion of glycerol in the sequencing reactions yields greatly improved results for some primer and template combinations. The inclusion of (alpha) -Thio-dNTP's in the labeling reaction increases signal intensity two- to three-fold.

DSAP: deep-sequencing small RNA analysis pipeline.

Science.gov (United States)

Huang, Po-Jung; Liu, Yi-Chung; Lee, Chi-Ching; Lin, Wei-Chen; Gan, Richie Ruei-Chi; Lyu, Ping-Chiang; Tang, Petrus

2010-07-01

DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log(2)-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw.

Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution.

Directory of Open Access Journals (Sweden)

Sara Imari Walker

Full Text Available Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for

Sequence dependent aggregation of peptides and fibril formation

Science.gov (United States)

Hung, Nguyen Ba; Le, Duy-Manh; Hoang, Trinh X.

2017-09-01

Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.

The sequence of spacers between the consensus sequences modulates the strength of procaryotic promoters

DEFF Research Database (Denmark)

Jensen, Peter Ruhdal; Hammer, Karin

1998-01-01

A library of synthetic promoters for Lactococcus lactis was constructed, in which the known consensus sequences were kept constant while the sequences of the separating spacers were randomized. The library consists of 38 promoters which differ in strength from 0.3 relative units, and up to more t......-reactors and cell factories....

Graphene nanodevices for DNA sequencing

NARCIS (Netherlands)

Heerema, S.J.; Dekker, C.

2016-01-01

Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data.

Science.gov (United States)

Massouras, Andreas; Decouttere, Frederik; Hens, Korneel; Deplancke, Bart

2010-07-01

High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently, software tools that facilitate such an incorporation should be of great interest. In this context, we developed WebPrInSeS, a web server tool allowing automated full-length clone sequence identification and verification using HTS data. WebPrInSeS encompasses two separate software applications. The first is WebPrInSeS-C which performs automated sequence verification of user-defined open-reading frame (ORF) clone libraries. The second is WebPrInSeS-E, which identifies positive hits in cDNA or ORF-based library screening experiments such as yeast one- or two-hybrid assays. Both tools perform de novo assembly using HTS data from any of the three major sequencing platforms. Thus, WebPrInSeS provides a highly integrated, cost-effective and efficient way to sequence-verify or identify clones of interest. WebPrInSeS is available at http://webprinses.epfl.ch/ and is open to all users.

Weak disorder in Fibonacci sequences

Energy Technology Data Exchange (ETDEWEB)

Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

2006-05-19

We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

Directory of Open Access Journals (Sweden)

Yan Wei Lim

2014-08-01

Full Text Available Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.

Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

Directory of Open Access Journals (Sweden)

Xu Xiangming

2010-12-01

Full Text Available Abstract Background Determining the position and order of contigs and scaffolds from a genome assembly within an organism's genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method. Results The strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for V. inaequalis and F. vesca, respectively, to genetic linkage maps. Conclusions We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.

Next-Generation Sequencing in the Mycology Lab.

Science.gov (United States)

Zoll, Jan; Snelders, Eveline; Verweij, Paul E; Melchers, Willem J G

New state-of-the-art techniques in sequencing offer valuable tools in both detection of mycobiota and in understanding of the molecular mechanisms of resistance against antifungal compounds and virulence. Introduction of new sequencing platform with enhanced capacity and a reduction in costs for sequence analysis provides a potential powerful tool in mycological diagnosis and research. In this review, we summarize the applications of next-generation sequencing techniques in mycology.

Finding the most significant common sequence and structure motifs in a set of RNA sequences

DEFF Research Database (Denmark)

Gorodkin, Jan; Heyer, L.J.; Stormo, G.D.

1997-01-01

We present a computational scheme to locally align a collection of RNA sequences using sequence and structure constraints, In addition, the method searches for the resulting alignments with the most significant common motifs, among all possible collections, The first part utilizes a simplified...

Comparing Whole-Genome Sequencing with Sanger Sequencing for spa Typing of Methicillin-Resistant Staphylococcus aureus

DEFF Research Database (Denmark)

Bartels, Mette Damkjaer; Petersen, Andreas; Worning, Peder

2014-01-01

spa typing of methicillin-resistant Staphylococcus aureus (MRSA) has traditionally been done by PCR amplification and Sanger sequencing of the spa repeat region. At Hvidovre Hospital, Denmark, whole-genome sequencing (WGS) of all MRSA isolates has been performed routinely since January 2013, and ...

Electricity sequence control

International Nuclear Information System (INIS)

Shin, Heung Ryeol

2010-03-01

The contents of the book are introduction of control system, like classification and control signal, introduction of electricity power switch, such as push-button and detection switch sensor for induction type and capacitance type machinery for control, solenoid valve, expression of sequence and type of electricity circuit about using diagram, time chart, marking and term, logic circuit like Yes, No, and, or and equivalence logic, basic electricity circuit, electricity sequence control, added condition, special program control about choice and jump of program, motor control, extra circuit on repeat circuit, pause circuit in a conveyer, safety regulations and rule about classification of electricity disaster and protective device for insulation.

High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform

DEFF Research Database (Denmark)

Fordyce, Sarah Louise; Avila Arcos, Maria del Carmen; Rockenbauer, Eszter

2011-01-01

repeat units. These methods do not allow for the full resolution of STR base composition that sequencing approaches could provide. Here we present an STR profiling method based on the use of the Roche Genome Sequencer (GS) FLX to simultaneously sequence multiple core STR loci. Using this method...

A genome-wide analysis of lentivector integration sites using targeted sequence capture and next generation sequencing technology.

Science.gov (United States)

Ustek, Duran; Sirma, Sema; Gumus, Ergun; Arikan, Muzaffer; Cakiris, Aris; Abaci, Neslihan; Mathew, Jaicy; Emrence, Zeliha; Azakli, Hulya; Cosan, Fulya; Cakar, Atilla; Parlak, Mahmut; Kursun, Olcay

2012-10-01

One application of next-generation sequencing (NGS) is the targeted resequencing of interested genes which has not been used in viral integration site analysis of gene therapy applications. Here, we combined targeted sequence capture array and next generation sequencing to address the whole genome profiling of viral integration sites. Human 293T and K562 cells were transduced with a HIV-1 derived vector. A custom made DNA probe sets targeted pLVTHM vector used to capture lentiviral vector/human genome junctions. The captured DNA was sequenced using GS FLX platform. Seven thousand four hundred and eighty four human genome sequences flanking the long terminal repeats (LTR) of pLVTHM fragment sequences matched with an identity of at least 98% and minimum 50 bp criteria in both cells. In total, 203 unique integration sites were identified. The integrations in both cell lines were totally distant from the CpG islands and from the transcription start sites and preferentially located in introns. A comparison between the two cell lines showed that the lentiviral-transduced DNA does not have the same preferred regions in the two different cell lines. Copyright © 2012 Elsevier B.V. All rights reserved.

ϕ-statistically quasi Cauchy sequences

Directory of Open Access Journals (Sweden)

Bipan Hazarika

2016-04-01

Full Text Available Let P denote the space whose elements are finite sets of distinct positive integers. Given any element σ of P, we denote by p(σ the sequence {pn(σ} such that pn(σ=1 for n ∈ σ and pn(σ=0 otherwise. Further Ps={σ∈P:∑n=1∞pn(σ≤s}, i.e. Ps is the set of those σ whose support has cardinality at most s. Let (ϕn be a non-decreasing sequence of positive integers such that nϕn+1≤(n+1ϕn for all n∈N and the class of all sequences (ϕn is denoted by Φ. Let E⊆N. The number δϕ(E=lims→∞1ϕs|{k∈σ,σ∈Ps:k∈E}| is said to be the ϕ-density of E. A sequence (xn of points in R is ϕ-statistically convergent (or Sϕ-convergent to a real number ℓ for every ε > 0 if the set {n∈N:|xn−ℓ|≥ɛ} has ϕ-density zero. We introduce ϕ-statistically ward continuity of a real function. A real function is ϕ-statistically ward continuous if it preserves ϕ-statistically quasi Cauchy sequences where a sequence (xn is called to be ϕ-statistically quasi Cauchy (or Sϕ-quasi Cauchy when (Δxn=(xn+1−xn is ϕ-statistically convergent to 0. i.e. a sequence (xn of points in R is called ϕ-statistically quasi Cauchy (or Sϕ-quasi Cauchy for every ε > 0 if {n∈N:|xn+1−xn|≥ɛ} has ϕ-density zero. Also we introduce the concept of ϕ-statistically ward compactness and obtain results related to ϕ-statistically ward continuity, ϕ-statistically ward compactness, statistically ward continuity, ward continuity, ward compactness, ordinary compactness, uniform continuity, ordinary continuity, δ-ward continuity, and slowly oscillating continuity.

In silico Analysis of 3′-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

Science.gov (United States)

Tanaka, Mizuki; Sakai, Yoshifumi; Yamada, Osamu; Shintani, Takahiro; Gomi, Katsuya

2011-01-01

To investigate 3′-end-processing signals in Aspergillus oryzae, we created a nucleotide sequence data set of the 3′-untranslated region (3′ UTR) plus 100 nucleotides (nt) sequence downstream of the poly(A) site using A. oryzae expressed sequence tags and genomic sequencing data. This data set comprised 1065 sequences derived from 1042 unique genes. The average 3′ UTR length in A. oryzae was 241 nt, which is greater than that in yeast but similar to that in plants. The 3′ UTR and 100 nt sequence downstream of the poly(A) site is notably U-rich, while the region located 15–30 nt upstream of the poly(A) site is markedly A-rich. The most frequently found hexanucleotide in this A-rich region is AAUGAA, although this sequence accounts for only 6% of all transcripts. These data suggested that A. oryzae has no highly conserved sequence element equivalent to AAUAAA, a mammalian polyadenylation signal. We identified that putative 3′-end-processing signals in A. oryzae, while less well conserved than those in mammals, comprised four sequence elements: the furthest upstream U-rich element, A-rich sequence, cleavage site, and downstream U-rich element flanking the cleavage site. Although these putative 3′-end-processing signals are similar to those in yeast and plants, some notable differences exist between them. PMID:21586533

Very high resolution single pass HLA genotyping using amplicon sequencing on the 454 next generation DNA sequencers: Comparison with Sanger sequencing.

Science.gov (United States)

Yamamoto, F; Höglund, B; Fernandez-Vina, M; Tyan, D; Rastrou, M; Williams, T; Moonsamy, P; Goodridge, D; Anderson, M; Erlich, H A; Holcomb, C L

2015-12-01

Compared to Sanger sequencing, next-generation sequencing offers advantages for high resolution HLA genotyping including increased throughput, lower cost, and reduced genotype ambiguity. Here we describe an enhancement of the Roche 454 GS GType HLA genotyping assay to provide very high resolution (VHR) typing, by the addition of 8 primer pairs to the original 14, to genotype 11 HLA loci. These additional amplicons help resolve common and well-documented alleles and exclude commonly found null alleles in genotype ambiguity strings. Simplification of workflow to reduce the initial preparation effort using early pooling of amplicons or the Fluidigm Access Array™ is also described. Performance of the VHR assay was evaluated on 28 well characterized cell lines using Conexio Assign MPS software which uses genomic, rather than cDNA, reference sequence. Concordance was 98.4%; 1.6% had no genotype assignment. Of concordant calls, 53% were unambiguous. To further assess the assay, 59 clinical samples were genotyped and results compared to unambiguous allele assignments obtained by prior sequence-based typing supplemented with SSO and/or SSP. Concordance was 98.7% with 58.2% as unambiguous calls; 1.3% could not be assigned. Our results show that the amplicon-based VHR assay is robust and can replace current Sanger methodology. Together with software enhancements, it has the potential to provide even higher resolution HLA typing. Copyright © 2015. Published by Elsevier Inc.

Tournaments, oriented graphs and football sequences

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Pirzada S.

2017-08-01

Full Text Available Consider the result of a soccer league competition where n teams play each other exactly once. A team gets three points for each win and one point for each draw. The total score obtained by each team vi is called the f-score of vi and is denoted by fi. The sequences of all f-scores [fi]i=1n$\\left[ {{\\rm{f}}_{\\rm{i}} } \\right]_{{\\rm{i}} = 1}^{\\rm{n}} $ arranged in non-decreasing order is called the f-score sequence of the competition. We raise the following problem: Which sequences of non-negative integers in non-decreasing order is a football sequence, that is the outcome of a soccer league competition. We model such a competition by an oriented graph with teams represented by vertices in which the teams play each other once, with an arc from team u to team v if and only if u defeats v. We obtain some necessary conditions for football sequences and some characterizations under restrictions.

Geoseq: a tool for dissecting deep-sequencing datasets

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Homann Robert

2010-10-01

Full Text Available Abstract Background Datasets generated on deep-sequencing platforms have been deposited in various public repositories such as the Gene Expression Omnibus (GEO, Sequence Read Archive (SRA hosted by the NCBI, or the DNA Data Bank of Japan (ddbj. Despite being rich data sources, they have not been used much due to the difficulty in locating and analyzing datasets of interest. Results Geoseq http://geoseq.mssm.edu provides a new method of analyzing short reads from deep sequencing experiments. Instead of mapping the reads to reference genomes or sequences, Geoseq maps a reference sequence against the sequencing data. It is web-based, and holds pre-computed data from public libraries. The analysis reduces the input sequence to tiles and measures the coverage of each tile in a sequence library through the use of suffix arrays. The user can upload custom target sequences or use gene/miRNA names for the search and get back results as plots and spreadsheet files. Geoseq organizes the public sequencing data using a controlled vocabulary, allowing identification of relevant libraries by organism, tissue and type of experiment. Conclusions Analysis of small sets of sequences against deep-sequencing datasets, as well as identification of public datasets of interest, is simplified by Geoseq. We applied Geoseq to, a identify differential isoform expression in mRNA-seq datasets, b identify miRNAs (microRNAs in libraries, and identify mature and star sequences in miRNAS and c to identify potentially mis-annotated miRNAs. The ease of using Geoseq for these analyses suggests its utility and uniqueness as an analysis tool.

DNA sequence modeling based on context trees

NARCIS (Netherlands)

Kusters, C.J.; Ignatenko, T.; Roland, J.; Horlin, F.

2015-01-01

Genomic sequences contain instructions for protein and cell production. Therefore understanding and identification of biologically and functionally meaningful patterns in DNA sequences is of paramount importance. Modeling of DNA sequences in its turn can help to better understand and identify such

A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants

NARCIS (Netherlands)

Ho, Cynthia K. Y.; Welkers, Matthijs R. A.; Thomas, Xiomara V.; Sullivan, James C.; Kieffer, Tara L.; Reesink, Henk W.; Rebers, Sjoerd P. H.; de Jong, Menno D.; Schinkel, Janke; Molenkamp, Richard

2015-01-01

We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

DEFF Research Database (Denmark)

Havgaard, Jakob Hull; Lyngsø, Rune B.; Stormo, Gary D.

2005-01-01

detect two genes with low sequence similarity, where the genes are part of a larger genomic region. Results: Here we present such an approach for pairwise local alignment which is based on FILDALIGN and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include...... the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy....... The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. Availability...

Volcanic influence of Mt. Fuji on the watershed of Lake Motosu and its impact on the lacustrine sedimentary record

Science.gov (United States)

Lamair, Laura; Hubert-Ferrari, Aurélia; Yamamoto, Shinya; El Ouahabi, Meriam; Vander Auwera, Jacqueline; Obrochta, Stephen; Boes, Evelien; Nakamura, Atsunori; Fujiwara, Osamu; Shishikura, Masanobu; Schmidt, Sabine; Siani, Giuseppe; Miyairi, Yosuke; Yokoyama, Yusuke; De Batist, Marc; Heyvaert, Vanessa M. A.; QuakeRecNankai Team

2018-01-01

Lacustrine sediments are particularly sensitive to modifications within the lake catchment. In a volcanic area, sedimentation rates are directly affected by the history of the volcano and its eruptions. Here, we investigate the impact of Mt. Fuji Volcano (Japan) on Lake Motosu and its watershed. The lacustrine infill is studied by combining seismic reflection profiles and sediment cores. We show evidence of changes in sedimentation patterns during the depositional history of Lake Motosu. The frequency of large mass-transport deposits recorded within the lake decreases over the Holocene. Before 8000 cal yr BP, large sublacustrine landslides and turbidites were filling the lacustrine depression. After 8000 cal yr BP, only one large sublacustrine landslide was recorded. The change in sedimentation pattern coincides with a change in sediment accumulation rate. Over the last 8000 cal yr BP, the sediment accumulation rate was not sufficient enough to produce large sublacustrine slope failures. Consequently, the frequency of large mass-transport deposits decreased and only turbidites resulting from surficial slope reworking occurred. These constitute the main sedimentary infill of the deep basin. We link the change in sediment accumulation rate with (i) climate and vegetation changes; and (ii) the Mt. Fuji eruptions which affected the Lake Motosu watershed by reducing its size and strongly modified its topography. Moreover, this study highlights that the deposition of turbidites in the deep basin of Lake Motosu is mainly controlled by the paleobathymetry of the lakefloor. Two large mass-transport deposits, occurring around 8000 cal yr BP and 2000 cal yr BP respectively, modified the paleobathymetry of the lakefloor and therefore changed the turbidite depositional pattern of Lake Motosu.

Low-Energy Electron-Induced Strand Breaks in Telomere-Derived DNA Sequences-Influence of DNA Sequence and Topology.

Science.gov (United States)

Rackwitz, Jenny; Bald, Ilko

2018-03-26

During cancer radiation therapy high-energy radiation is used to reduce tumour tissue. The irradiation produces a shower of secondary low-energy (DNA very efficiently by dissociative electron attachment. Recently, it was suggested that low-energy electron-induced DNA strand breaks strongly depend on the specific DNA sequence with a high sensitivity of G-rich sequences. Here, we use DNA origami platforms to expose G-rich telomere sequences to low-energy (8.8 eV) electrons to determine absolute cross sections for strand breakage and to study the influence of sequence modifications and topology of telomeric DNA on the strand breakage. We find that the telomeric DNA 5'-(TTA GGG) 2 is more sensitive to low-energy electrons than an intermixed sequence 5'-(TGT GTG A) 2 confirming the unique electronic properties resulting from G-stacking. With increasing length of the oligonucleotide (i.e., going from 5'-(GGG ATT) 2 to 5'-(GGG ATT) 4 ), both the variety of topology and the electron-induced strand break cross sections increase. Addition of K + ions decreases the strand break cross section for all sequences that are able to fold G-quadruplexes or G-intermediates, whereas the strand break cross section for the intermixed sequence remains unchanged. These results indicate that telomeric DNA is rather sensitive towards low-energy electron-induced strand breakage suggesting significant telomere shortening that can also occur during cancer radiation therapy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Geomorphic response of a continental margin to tectonic and eustatic variations, the Levant margin during the Messinian Salinity Crisis

Science.gov (United States)

Ben Moshe, Liran; Ben-Avraham, Zvi; Enzel, Yehouda; Uri, Schattner

2017-04-01

During the Messinian Salinity Crisis (MSC, 5.97±0.01-5.33 Ma) the Mediterranean Levant margin experienced major eustatic and sedimentary cycles as well as tectonic motion along the nearby Dead Sea fault plate boundary. New structures formed along this margin with morphology responding to these changes. Our study focuses on changes in this morphology across the margin. It is based on interpretation of three 3D seismic reflection volumes from offshore Israel. Multi-attribute analysis aided the extraction of key reflectors. Morphologic analysis of these data quantified interacting eustasy, sedimentation, and tectonics. Late Messinian morphologic domains include: (a) continental shelf; (b) 'Delta' anticline, forming a ridge diagonal to the strike of the margin; (c) southward dipping 'Hadera' valley, separating between (a) and (b); (d) 'Delta Gap' - a water gap crossing perpendicular to the anticline axis, exhibiting a sinuous thalweg; (e) continental slope. Drainage across the margin developed in several stages. Remains of turbidite flows crossing the margin down-slope were spotted across the 'Delta' anticline. These flows accumulated with the MSC evaporate sequence and prior to the anticline folding. Rising of the anticline, above the then bathymetry, either blocked or diverted the turbidites. That rising also defined the Hadera valley. In-situ evaporates, covering the valley floor, are, in turn covered by a fan-delta at the distal end of the valley. The fan-delta complex contains eroded evaporites and Lago-Mare fauna. Its top is truncated by dendritic fluvial channels that drained towards the Delta Gap. The Delta Gap was carved through the Delta ridge in a morphological and structural transition zone. We propose that during the first stages of the MSC (5.97±0.01-5.59 ma) destabilization of the continental slope due to oscillating sea level produced gravity currents that flowed through the pre-existing Delta anticline. Subsequent folding of the Delta anticline

Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences

DEFF Research Database (Denmark)

Karlskov-Mortensen, Peter; Hu, Z.L.; Gorodkin, Jan

2007-01-01

the human genome (BLAST cut-off threshold = 1 x 10-5). All microsatellite sequences placed on the comparative map are accessible at http://www.animalgenome.org/QTLdb/pig.html . These sequences increase the number of identified microsatellites in the porcine genome by several orders of magnitude...

LPTAU, Quasi Random Sequence Generator

International Nuclear Information System (INIS)

Sobol, Ilya M.

1993-01-01

1 - Description of program or function: LPTAU generates quasi random sequences. These are uniformly distributed sets of L=M N points in the N-dimensional unit cube: I N =[0,1]x...x[0,1]. These sequences are used as nodes for multidimensional integration; as searching points in global optimization; as trial points in multi-criteria decision making; as quasi-random points for quasi Monte Carlo algorithms. 2 - Method of solution: Uses LP-TAU sequence generation (see references). 3 - Restrictions on the complexity of the problem: The number of points that can be generated is L 30 . The dimension of the space cannot exceed 51

Main sequence mass loss

International Nuclear Information System (INIS)

Brunish, W.M.; Guzik, J.A.; Willson, L.A.; Bowen, G.

1987-01-01

It has been hypothesized that variable stars may experience mass loss, driven, at least in part, by oscillations. The class of stars we are discussing here are the δ Scuti variables. These are variable stars with masses between about 1.2 and 2.25 M/sub θ/, lying on or very near the main sequence. According to this theory, high rotation rates enhance the rate of mass loss, so main sequence stars born in this mass range would have a range of mass loss rates, depending on their initial rotation velocity and the amplitude of the oscillations. The stars would evolve rapidly down the main sequence until (at about 1.25 M/sub θ/) a surface convection zone began to form. The presence of this convective region would slow the rotation, perhaps allowing magnetic braking to occur, and thus sharply reduce the mass loss rate. 7 refs

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.

Sequencing intractable DNA to close microbial genomes.

Directory of Open Access Journals (Sweden)

Richard A Hurt

Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

Sequencing Intractable DNA to Close Microbial Genomes

Energy Technology Data Exchange (ETDEWEB)

Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

2012-01-01

Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

Commercial Art: Scope and Sequence.

Science.gov (United States)

Nashville - Davidson County Metropolitan Public Schools, TN.

This scope and sequence guide, developed for a commercial art vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

Divide and conquer: enriching environmental sequencing data.

Directory of Open Access Journals (Sweden)

Anne Bergeron

2007-09-01

Full Text Available In environmental sequencing projects, a mix of DNA from a whole microbial community is fragmented and sequenced, with one of the possible goals being to reconstruct partial or complete genomes of members of the community. In communities with high diversity of species, a significant proportion of the sequences do not overlap any other fragment in the sample. This problem will arise not only in situations with a relatively even distribution of many species, but also when the community in a particular environment is routinely dominated by the same few species. In the former case, no genomes may be assembled at all, while in the latter case a few dominant species in an environment will always be sequenced at high coverage to the detriment of coverage of the greater number of sparse species.Here we show that, with the same global sequencing effort, separating the species into two or more sub-communities prior to sequencing can yield a much higher proportion of sequences that can be assembled. We first use the Lander-Waterman model to show that, if the expected percentage of singleton sequences is higher than 25%, then, under the uniform distribution hypothesis, splitting the community is always a wise choice. We then construct simulated microbial communities to show that the results hold for highly non-uniform distributions. We also show that, for the distributions considered in the experiments, it is possible to estimate quite accurately the relative diversity of the two sub-communities.Given the fact that several methods exist to split microbial communities based on physical properties such as size, density, surface biochemistry, or optical properties, we strongly suggest that groups involved in environmental sequencing, and expecting high diversity, consider splitting their communities in order to maximize the information content of their sequencing effort.

How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes

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Alevtina Ruban

2017-10-01

Full Text Available Accessory, supernumerary, or—most simply—B chromosomes, are found in many eukaryotic karyotypes. These small chromosomes do not follow the usual pattern of segregation, but rather are transmitted in a higher than expected frequency. As increasingly being demonstrated by next-generation sequencing (NGS, their structure comprises fragments of standard (A chromosomes, although in some plant species, their sequence also includes contributions from organellar genomes. Transcriptomic analyses of various animal and plant species have revealed that, contrary to what used to be the common belief, some of the B chromosome DNA is protein-encoding. This review summarizes the progress in understanding B chromosome biology enabled by the application of next-generation sequencing technology and state-of-the-art bioinformatics. In particular, a contrast is drawn between a direct sequencing approach and a strategy based on a comparative genomics as alternative routes that can be taken towards the identification of B chromosome sequences.

Management of High-Throughput DNA Sequencing Projects: Alpheus.

Science.gov (United States)

Miller, Neil A; Kingsmore, Stephen F; Farmer, Andrew; Langley, Raymond J; Mudge, Joann; Crow, John A; Gonzalez, Alvaro J; Schilkey, Faye D; Kim, Ryan J; van Velkinburgh, Jennifer; May, Gregory D; Black, C Forrest; Myers, M Kathy; Utsey, John P; Frost, Nicholas S; Sugarbaker, David J; Bueno, Raphael; Gullans, Stephen R; Baxter, Susan M; Day, Steve W; Retzel, Ernest F

2008-12-26

High-throughput DNA sequencing has enabled systems biology to begin to address areas in health, agricultural and basic biological research. Concomitant with the opportunities is an absolute necessity to manage significant volumes of high-dimensional and inter-related data and analysis. Alpheus is an analysis pipeline, database and visualization software for use with massively parallel DNA sequencing technologies that feature multi-gigabase throughput characterized by relatively short reads, such as Illumina-Solexa (sequencing-by-synthesis), Roche-454 (pyrosequencing) and Applied Biosystem's SOLiD (sequencing-by-ligation). Alpheus enables alignment to reference sequence(s), detection of variants and enumeration of sequence abundance, including expression levels in transcriptome sequence. Alpheus is able to detect several types of variants, including non-synonymous and synonymous single nucleotide polymorphisms (SNPs), insertions/deletions (indels), premature stop codons, and splice isoforms. Variant detection is aided by the ability to filter variant calls based on consistency, expected allele frequency, sequence quality, coverage, and variant type in order to minimize false positives while maximizing the identification of true positives. Alpheus also enables comparisons of genes with variants between cases and controls or bulk segregant pools. Sequence-based differential expression comparisons can be developed, with data export to SAS JMP Genomics for statistical analysis.

Sequencing and comparing whole mitochondrial genomes ofanimals

Energy Technology Data Exchange (ETDEWEB)

Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

2005-04-22

Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

Comparison of next generation sequencing technologies for transcriptome characterization

Directory of Open Access Journals (Sweden)

Soltis Douglas E

2009-08-01

Full Text Available Abstract Background We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the Arabidopsis genome (NCBI Accession SRA008180.19. We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica and the magnoliid avocado (Persea americana using a variety of methods for cDNA synthesis. Results The Arabidopsis reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB, 119,518 (88.7% mapped exactly to known exons, while 1,117 (0.8% mapped to introns, 11,524 (8.6% spanned annotated intron/exon boundaries, and 3,066 (2.3% extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The Arabidopsis data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc http://fgp.huck.psu.edu/NG_Sims/ngsim.pl, an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics. Conclusion NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance

Spatio-temporal alignment of pedobarographic image sequences.

Science.gov (United States)

Oliveira, Francisco P M; Sousa, Andreia; Santos, Rubim; Tavares, João Manuel R S

2011-07-01

This article presents a methodology to align plantar pressure image sequences simultaneously in time and space. The spatial position and orientation of a foot in a sequence are changed to match the foot represented in a second sequence. Simultaneously with the spatial alignment, the temporal scale of the first sequence is transformed with the aim of synchronizing the two input footsteps. Consequently, the spatial correspondence of the foot regions along the sequences as well as the temporal synchronizing is automatically attained, making the study easier and more straightforward. In terms of spatial alignment, the methodology can use one of four possible geometric transformation models: rigid, similarity, affine, or projective. In the temporal alignment, a polynomial transformation up to the 4th degree can be adopted in order to model linear and curved time behaviors. Suitable geometric and temporal transformations are found by minimizing the mean squared error (MSE) between the input sequences. The methodology was tested on a set of real image sequences acquired from a common pedobarographic device. When used in experimental cases generated by applying geometric and temporal control transformations, the methodology revealed high accuracy. In addition, the intra-subject alignment tests from real plantar pressure image sequences showed that the curved temporal models produced better MSE results (P alignment of pedobarographic image data, since previous methods can only be applied on static images.

Intra-species sequence comparisons for annotating genomes

Energy Technology Data Exchange (ETDEWEB)

Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

2004-07-15

Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

Information decomposition method to analyze symbolical sequences

International Nuclear Information System (INIS)

Korotkov, E.V.; Korotkova, M.A.; Kudryashov, N.A.

2003-01-01

The information decomposition (ID) method to analyze symbolical sequences is presented. This method allows us to reveal a latent periodicity of any symbolical sequence. The ID method is shown to have advantages in comparison with application of the Fourier transformation, the wavelet transform and the dynamic programming method to look for latent periodicity. Examples of the latent periods for poetic texts, DNA sequences and amino acids are presented. Possible origin of a latent periodicity for different symbolical sequences is discussed

Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.).

Science.gov (United States)

Cloutier, Sylvie; Miranda, Evelyn; Ward, Kerry; Radovanovic, Natasa; Reimer, Elsa; Walichnowski, Andrzej; Datla, Raju; Rowland, Gordon; Duguid, Scott; Ragupathy, Raja

2012-08-01

Flax is an important oilseed crop in North America and is mostly grown as a fibre crop in Europe. As a self-pollinated diploid with a small estimated genome size of ~370 Mb, flax is well suited for fast progress in genomics. In the last few years, important genetic resources have been developed for this crop. Here, we describe the assessment and comparative analyses of 1,506 putative simple sequence repeats (SSRs) of which, 1,164 were derived from BAC-end sequences (BESs) and 342 from expressed sequence tags (ESTs). The SSRs were assessed on a panel of 16 flax accessions with 673 (58 %) and 145 (42 %) primer pairs being polymorphic in the BESs and ESTs, respectively. With 818 novel polymorphic SSR primer pairs reported in this study, the repertoire of available SSRs in flax has more than doubled from the combined total of 508 of all previous reports. Among nucleotide motifs, trinucleotides were the most abundant irrespective of the class, but dinucleotides were the most polymorphic. SSR length was also positively correlated with polymorphism. Two dinucleotide (AT/TA and AG/GA) and two trinucleotide (AAT/ATA/TAA and GAA/AGA/AAG) motifs and their iterations, different from those reported in many other crops, accounted for more than half of all the SSRs and were also more polymorphic (63.4 %) than the rest of the markers (42.7 %). This improved resource promises to be useful in genetic, quantitative trait loci (QTL) and association mapping as well as for anchoring the physical/genetic map with the whole genome shotgun reference sequence of flax.

A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences

Science.gov (United States)

Caramelli, David; Milani, Lucio; Vai, Stefania; Modi, Alessandra; Pecchioli, Elena; Girardi, Matteo; Pilli, Elena; Lari, Martina; Lippi, Barbara; Ronchitelli, Annamaria; Mallegni, Francesco; Casoli, Antonella; Bertorelle, Giorgio; Barbujani, Guido

2008-01-01

Background DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans. Methodology/Principal Findings We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences. Conclusions/Significance: The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans. PMID:18628960

A 28,000 years old Cro-Magnon mtDNA sequence differs from all potentially contaminating modern sequences.

Directory of Open Access Journals (Sweden)

David Caramelli

Full Text Available BACKGROUND: DNA sequences from ancient specimens may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal and early modern (Cro-Magnoid Europeans. METHODOLOGY/PRINCIPAL FINDINGS: We typed the mitochondrial DNA (mtDNA hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23 and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences. CONCLUSIONS/SIGNIFICANCE: The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.

Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

Science.gov (United States)

Desai, Aarti; Marwah, Veer Singh; Yadav, Akshay; Jha, Vineet; Dhaygude, Kishor; Bangar, Ujwala; Kulkarni, Vivek; Jere, Abhay

2013-01-01

Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects, especially in de novo genome sequencing. Currently, NGS systems generate sequence data as short reads and de novo genome assembly using these short reads is computationally very intensive. Due to lower cost of sequencing and higher throughput, NGS systems now provide the ability to sequence genomes at high depth. However, currently no report is available highlighting the impact of high sequence depth on genome assembly using real data sets and multiple assembly algorithms. Recently, some studies have evaluated the impact of sequence coverage, error rate and average read length on genome assembly using multiple assembly algorithms, however, these evaluations were performed using simulated datasets. One limitation of using simulated datasets is that variables such as error rates, read length and coverage which are known to impact genome assembly are carefully controlled. Hence, this study was undertaken to identify the minimum depth of sequencing required for de novo assembly for different sized genomes using graph based assembly algorithms and real datasets. Illumina reads for E.coli (4.6 MB) S.kudriavzevii (11.18 MB) and C.elegans (100 MB) were assembled using SOAPdenovo, Velvet, ABySS, Meraculous and IDBA-UD. Our analysis shows that 50X is the optimum read depth for assembling these genomes using all assemblers except Meraculous which requires 100X read depth. Moreover, our analysis shows that de novo assembly from 50X read data requires only 6-40 GB RAM depending on the genome size and assembly algorithm used. We believe that this information can be extremely valuable for researchers in designing experiments and multiplexing which will enable optimum utilization of sequencing as well as analysis resources.

Identification of genomic insertion and flanking sequence of G2-EPSPS and GAT transgenes in soybean using whole genome sequencing method

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Bingfu Guo

2016-07-01

Full Text Available Molecular characterization of sequences flanking exogenous fragment insertions is essential for safety assessment and labeling of genetically modified organisms (GMO. In this study, the T-DNA insertion sites and flanking sequences were identified in two newly developed transgenic glyphosate-tolerant soybeans GE-J16 and ZH10-6 based on whole genome sequencing (WGS method. About 21 Gb sequence data (~21× coverage for each line was generated on Illumina HiSeq 2500 platform. The junction reads mapped to boundary of T-DNA and flanking sequences in these two events were identified by comparing all sequencing reads with soybean reference genome and sequence of transgenic vector. The putative insertion loci and flanking sequences were further confirmed by PCR amplification, Sanger sequencing, and co-segregation analysis. All these analyses supported that exogenous T-DNA fragments were integrated in positions of Chr19: 50543767-50543792 and Chr17: 7980527-7980541 in these two transgenic lines. Identification of the genomic insertion site of the G2-EPSPS and GAT transgenes will facilitate the use of their glyphosate-tolerant traits in soybean breeding program. These results also demonstrated that WGS is a cost-effective and rapid method of identifying sites of T-DNA insertions and flanking sequences in soybean.

Leaf sequencing algorithms for segmented multileaf collimation

International Nuclear Information System (INIS)

Kamath, Srijit; Sahni, Sartaj; Li, Jonathan; Palta, Jatinder; Ranka, Sanjay

2003-01-01

The delivery of intensity-modulated radiation therapy (IMRT) with a multileaf collimator (MLC) requires the conversion of a radiation fluence map into a leaf sequence file that controls the movement of the MLC during radiation delivery. It is imperative that the fluence map delivered using the leaf sequence file is as close as possible to the fluence map generated by the dose optimization algorithm, while satisfying hardware constraints of the delivery system. Optimization of the leaf sequencing algorithm has been the subject of several recent investigations. In this work, we present a systematic study of the optimization of leaf sequencing algorithms for segmental multileaf collimator beam delivery and provide rigorous mathematical proofs of optimized leaf sequence settings in terms of monitor unit (MU) efficiency under most common leaf movement constraints that include minimum leaf separation constraint and leaf interdigitation constraint. Our analytical analysis shows that leaf sequencing based on unidirectional movement of the MLC leaves is as MU efficient as bidirectional movement of the MLC leaves

Leaf sequencing algorithms for segmented multileaf collimation

Energy Technology Data Exchange (ETDEWEB)

Kamath, Srijit [Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL (United States); Sahni, Sartaj [Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL (United States); Li, Jonathan [Department of Radiation Oncology, University of Florida, Gainesville, FL (United States); Palta, Jatinder [Department of Radiation Oncology, University of Florida, Gainesville, FL (United States); Ranka, Sanjay [Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL (United States)

2003-02-07

The delivery of intensity-modulated radiation therapy (IMRT) with a multileaf collimator (MLC) requires the conversion of a radiation fluence map into a leaf sequence file that controls the movement of the MLC during radiation delivery. It is imperative that the fluence map delivered using the leaf sequence file is as close as possible to the fluence map generated by the dose optimization algorithm, while satisfying hardware constraints of the delivery system. Optimization of the leaf sequencing algorithm has been the subject of several recent investigations. In this work, we present a systematic study of the optimization of leaf sequencing algorithms for segmental multileaf collimator beam delivery and provide rigorous mathematical proofs of optimized leaf sequence settings in terms of monitor unit (MU) efficiency under most common leaf movement constraints that include minimum leaf separation constraint and leaf interdigitation constraint. Our analytical analysis shows that leaf sequencing based on unidirectional movement of the MLC leaves is as MU efficient as bidirectional movement of the MLC leaves.

Palaeoenvironment of Eocene prodelta in Spitsbergen recorded by the trace fossil Phycosiphon incertum

Directory of Open Access Journals (Sweden)

Francisco Javier Rodríguez-Tovar

2014-10-01

Full Text Available Ichnological, sedimentological and geochemical analyses were conducted on the Eocene Frysjaodden Formation in order to interpret palaeoenvironment prodelta sediments in the Central Basin of Spitsbergen. Phycosiphon incertum is the exclusive ichnotaxon showing differences in size, distribution, abundance and density, and relation to laminated/bioturbated intervals. Large P. incertum mainly occur dispersed, isolated and randomly distributed throughout the weakly laminated/non-laminated intervals. Small P. incertum occur occasionally in patches of several burrows within laminated intervals or as densely packed burrows in thin horizons in laminated intervals or constituting fully bioturbated intervals that are several centimetres thick. Ichnological changes are mainly controlled by oxygenation, although the availability of benthic food cannot be discarded. Changes in oxygenation and rate of sedimentation can be correlated with the registered variations in the Bouma sequence of the distal turbiditic beds within prodeltal shelf sediments.

Genome Sequencing and Analysis Conference IV

Energy Technology Data Exchange (ETDEWEB)

1993-12-31

J. Craig Venter and C. Thomas Caskey co-chaired Genome Sequencing and Analysis Conference IV held at Hilton Head, South Carolina from September 26--30, 1992. Venter opened the conference by noting that approximately 400 researchers from 16 nations were present four times as many participants as at Genome Sequencing Conference I in 1989. Venter also introduced the Data Fair, a new component of the conference allowing exchange and on-site computer analysis of unpublished sequence data.

Sequencing BPS spectra

Energy Technology Data Exchange (ETDEWEB)

Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

2016-03-02

This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

Sequencing BPS spectra

International Nuclear Information System (INIS)

Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

2016-01-01

This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

On peculiar Šindel sequences

Czech Academy of Sciences Publication Activity Database

Křížek, Michal; Somer, L.

2010-01-01

Roč. 17, č. 2 (2010), s. 129-140 ISSN 0972-5555 R&D Projects: GA AV ČR(CZ) IAA100190803 Institutional research plan: CEZ:AV0Z10190503 Keywords : quadratic residue * Chinese remainder theorem * primitive Šindel sequences * Prague clock sequence Subject RIV: BA - General Mathematics http://www.pphmj.com/abstract/5095.htm

Fractals in DNA sequence analysis

Institute of Scientific and Technical Information of China (English)

Yu Zu-Guo(喻祖国); Vo Anh; Gong Zhi-Min(龚志民); Long Shun-Chao(龙顺潮)

2002-01-01

Fractal methods have been successfully used to study many problems in physics, mathematics, engineering, finance,and even in biology. There has been an increasing interest in unravelling the mysteries of DNA; for example, how can we distinguish coding and noncoding sequences, and the problems of classification and evolution relationship of organisms are key problems in bioinformatics. Although much research has been carried out by taking into consideration the long-range correlations in DNA sequences, and the global fractal dimension has been used in these works by other people, the models and methods are somewhat rough and the results are not satisfactory. In recent years, our group has introduced a time series model (statistical point of view) and a visual representation (geometrical point of view)to DNA sequence analysis. We have also used fractal dimension, correlation dimension, the Hurst exponent and the dimension spectrum (multifractal analysis) to discuss problems in this field. In this paper, we introduce these fractal models and methods and the results of DNA sequence analysis.

Attentional load and implicit sequence learning.

Science.gov (United States)

Shanks, David R; Rowland, Lee A; Ranger, Mandeep S

2005-06-01

A widely employed conceptualization of implicit learning hypothesizes that it makes minimal demands on attentional resources. This conjecture was investigated by comparing learning under single-task and dual-task conditions in the sequential reaction time (SRT) task. Participants learned probabilistic sequences, with dual-task participants additionally having to perform a counting task using stimuli that were targets in the SRT display. Both groups were then tested for sequence knowledge under single-task (Experiments 1 and 2) or dual-task (Experiment 3) conditions. Participants also completed a free generation task (Experiments 2 and 3) under inclusion or exclusion conditions to determine if sequence knowledge was conscious or unconscious in terms of its access to intentional control. The experiments revealed that the secondary task impaired sequence learning and that sequence knowledge was consciously accessible. These findings disconfirm both the notion that implicit learning is able to proceed normally under conditions of divided attention, and that the acquired knowledge is inaccessible to consciousness. A unitary framework for conceptualizing implicit and explicit learning is proposed.

Sequence of human protamine 2 cDNA

Energy Technology Data Exchange (ETDEWEB)

Domenjoud, L; Fronia, C; Uhde, F; Engel, W [Universitaet Goettingen (West Germany)

1988-08-11

The authors report the cloning and sequencing of a cDNA clone for human protamine 2 (hp2), isolated from a human testis cDNA library cloned in the vector {lambda}-gt11. A 66mer oligonucleotide, that corresponds to an amino acid sequence which is highly conserved between hp2 and mouse protamine 2 (mp2) served as hybridization probe. The homology between the amino acid sequence deduced from our cDNA and the published amino acid sequence for hp2 is 100%.

Snake Genome Sequencing: Results and Future Prospects.

Science.gov (United States)

Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

2016-12-01

Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

Snake Genome Sequencing: Results and Future Prospects

Directory of Open Access Journals (Sweden)

Harald M. I. Kerkkamp

2016-12-01

Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

High-Throughput Next-Generation Sequencing of Polioviruses

Science.gov (United States)

Montmayeur, Anna M.; Schmidt, Alexander; Zhao, Kun; Magaña, Laura; Iber, Jane; Castro, Christina J.; Chen, Qi; Henderson, Elizabeth; Ramos, Edward; Shaw, Jing; Tatusov, Roman L.; Dybdahl-Sissoko, Naomi; Endegue-Zanga, Marie Claire; Adeniji, Johnson A.; Oberste, M. Steven; Burns, Cara C.

2016-01-01

ABSTRACT The poliovirus (PV) is currently targeted for worldwide eradication and containment. Sanger-based sequencing of the viral protein 1 (VP1) capsid region is currently the standard method for PV surveillance. However, the whole-genome sequence is sometimes needed for higher resolution global surveillance. In this study, we optimized whole-genome sequencing protocols for poliovirus isolates and FTA cards using next-generation sequencing (NGS), aiming for high sequence coverage, efficiency, and throughput. We found that DNase treatment of poliovirus RNA followed by random reverse transcription (RT), amplification, and the use of the Nextera XT DNA library preparation kit produced significantly better results than other preparations. The average viral reads per total reads, a measurement of efficiency, was as high as 84.2% ± 15.6%. PV genomes covering >99 to 100% of the reference length were obtained and validated with Sanger sequencing. A total of 52 PV genomes were generated, multiplexing as many as 64 samples in a single Illumina MiSeq run. This high-throughput, sequence-independent NGS approach facilitated the detection of a diverse range of PVs, especially for those in vaccine-derived polioviruses (VDPV), circulating VDPV, or immunodeficiency-related VDPV. In contrast to results from previous studies on other viruses, our results showed that filtration and nuclease treatment did not discernibly increase the sequencing efficiency of PV isolates. However, DNase treatment after nucleic acid extraction to remove host DNA significantly improved the sequencing results. This NGS method has been successfully implemented to generate PV genomes for molecular epidemiology of the most recent PV isolates. Additionally, the ability to obtain full PV genomes from FTA cards will aid in facilitating global poliovirus surveillance. PMID:27927929

Sequence determinants of human microsatellite variability

Directory of Open Access Journals (Sweden)

Jakobsson Mattias

2009-12-01

Full Text Available Abstract Background Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database. Results Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length, under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity. Conclusions These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.

Sequence comparison and phylogenetic analysis of core gene of ...

African Journals Online (AJOL)

Phylogenetic analysis suggests that our sequences are clustered with sequences reported from Japan. This is the first phylogenetic analysis of HCV core gene from Pakistani population. Our sequences and sequences from Japan are grouped into same cluster in the phylogenetic tree. Sequence comparison and ...

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

Directory of Open Access Journals (Sweden)

Martin Mascher

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

HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.

Science.gov (United States)

Yin, Li; Yao, Jiqiang; Gardner, Brent P; Chang, Kaifen; Yu, Fahong; Goodenow, Maureen M

2012-01-01

Next Generation sequencing (NGS) applied to human papilloma viruses (HPV) can provide sensitive methods to investigate the molecular epidemiology of multiple type HPV infection. Currently a genotyping system with a comprehensive collection of updated HPV reference sequences and a capacity to handle NGS data sets is lacking. HPV-QUEST was developed as an automated and rapid HPV genotyping system. The web-based HPV-QUEST subtyping algorithm was developed using HTML, PHP, Perl scripting language, and MYSQL as the database backend. HPV-QUEST includes a database of annotated HPV reference sequences with updated nomenclature covering 5 genuses, 14 species and 150 mucosal and cutaneous types to genotype blasted query sequences. HPV-QUEST processes up to 10 megabases of sequences within 1 to 2 minutes. Results are reported in html, text and excel formats and display e-value, blast score, and local and coverage identities; provide genus, species, type, infection site and risk for the best matched reference HPV sequence; and produce results ready for additional analyses.

ON SOME RECURRENCE TYPE SMARANDACHE SEQUENCES

OpenAIRE

MAJUMDAR, A.A.K.; GUNARTO, H.

2000-01-01

In this paper, we study some properties of ten recurrence type Smarandache sequences, namely, the Smarandache odd, even, prime product, square product, higher-power product, permutation, consecutive, reverse, symmetric, and pierced chain sequences.

Protecting genomic sequence anonymity with generalization lattices.

Science.gov (United States)

Malin, B A

2005-01-01

Current genomic privacy technologies assume the identity of genomic sequence data is protected if personal information, such as demographics, are obscured, removed, or encrypted. While demographic features can directly compromise an individual's identity, recent research demonstrates such protections are insufficient because sequence data itself is susceptible to re-identification. To counteract this problem, we introduce an algorithm for anonymizing a collection of person-specific DNA sequences. The technique is termed DNA lattice anonymization (DNALA), and is based upon the formal privacy protection schema of k -anonymity. Under this model, it is impossible to observe or learn features that distinguish one genetic sequence from k-1 other entries in a collection. To maximize information retained in protected sequences, we incorporate a concept generalization lattice to learn the distance between two residues in a single nucleotide region. The lattice provides the most similar generalized concept for two residues (e.g. adenine and guanine are both purines). The method is tested and evaluated with several publicly available human population datasets ranging in size from 30 to 400 sequences. Our findings imply the anonymization schema is feasible for the protection of sequences privacy. The DNALA method is the first computational disclosure control technique for general DNA sequences. Given the computational nature of the method, guarantees of anonymity can be formally proven. There is room for improvement and validation, though this research provides the groundwork from which future researchers can construct genomics anonymization schemas tailored to specific datasharing scenarios.

Tracking TCRβ sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region

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Mark W Robinson

2016-04-01

Full Text Available To maintain a persistent infection viruses such as hepatitis C virus (HCV employ a range of mechanisms that subvert protective T cell responses. The suppression of antigen-specific T cell responses by HCV hinders efforts to profile T cell responses during chronic infection and antiviral therapy. Conventional methods of detecting antigen-specific T cells utilise either antigen stimulation (e.g. ELISpot, proliferation assays, cytokine production or antigen-loaded tetramer staining. This limits the ability to profile T cell responses during chronic infection due to suppressed effector function and the requirement for prior knowledge of antigenic viral peptide sequences. Recently high-throughput sequencing (HTS technologies have been developed for the analysis of T cell repertoires. In the present study we have assessed the feasibility of HTS of the TCRβ complementarity determining region (CDR3 to track T cell expansions in an antigen-independent manner. Using sequential blood samples from HCV-infected individuals undergoing anti-viral therapy we were able to measure the population frequencies of >35,000 TCRβ sequence clonotypes in each individual over the course of 12 weeks. TRBV/TRBJ gene segment usage varied markedly between individuals but remained relatively constant within individuals across the course of therapy. Despite this stable TRBV/TRBJ gene segment usage, a number of TCRβ sequence clonotypes showed dramatic changes in read frequency. These changes could not be linked to therapy outcomes in the present study however the TCRβ CDR3 sequences with the largest fold changes did include sequences with identical TRBV/TRBJ gene segment usage and high joining region homology to previously published CDR3 sequences from HCV-specific T cells targeting the HLA-B*0801-restricted 1395HSKKKCDEL1403 and HLA-A*0101–restricted 1435ATDALMTGY1443 epitopes. The pipeline developed in this proof of concept study provides a platform for the design of

Sequencing genes in silico using single nucleotide polymorphisms

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Zhang Xinyi

2012-01-01

Full Text Available Abstract Background The advent of high throughput sequencing technology has enabled the 1000 Genomes Project Pilot 3 to generate complete sequence data for more than 906 genes and 8,140 exons representing 697 subjects. The 1000 Genomes database provides a critical opportunity for further interpreting disease associations with single nucleotide polymorphisms (SNPs discovered from genetic association studies. Currently, direct sequencing of candidate genes or regions on a large number of subjects remains both cost- and time-prohibitive. Results To accelerate the translation from discovery to functional studies, we propose an in silico gene sequencing method (ISS, which predicts phased sequences of intragenic regions, using SNPs. The key underlying idea of our method is to infer diploid sequences (a pair of phased sequences/alleles at every functional locus utilizing the deep sequencing data from the 1000 Genomes Project and SNP data from the HapMap Project, and to build prediction models using flanking SNPs. Using this method, we have developed a database of prediction models for 611 known genes. Sequence prediction accuracy for these genes is 96.26% on average (ranges 79%-100%. This database of prediction models can be enhanced and scaled up to include new genes as the 1000 Genomes Project sequences additional genes on additional individuals. Applying our predictive model for the KCNJ11 gene to the Wellcome Trust Case Control Consortium (WTCCC Type 2 diabetes cohort, we demonstrate how the prediction of phased sequences inferred from GWAS SNP genotype data can be used to facilitate interpretation and identify a probable functional mechanism such as protein changes. Conclusions Prior to the general availability of routine sequencing of all subjects, the ISS method proposed here provides a time- and cost-effective approach to broadening the characterization of disease associated SNPs and regions, and facilitating the prioritization of candidate

Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species.

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Pietro Liò

Full Text Available A major goal of bioinformatics is the characterization of transcription factors and the transcriptional programs they regulate. Given the speed of genome sequencing, we would like to quickly annotate regulatory sequences in newly-sequenced genomes. In such cases, it would be helpful to predict sequence motifs by using experimental data from closely related model organism. Here we present a general algorithm that allow to identify transcription factor binding sites in one newly sequenced species by performing Bayesian regression on the annotated species. First we set the rationale of our method by applying it within the same species, then we extend it to use data available in closely related species. Finally, we generalise the method to handle the case when a certain number of experiments, from several species close to the species on which to make inference, are available. In order to show the performance of the method, we analyse three functionally related networks in the Ascomycota. Two gene network case studies are related to the G2/M phase of the Ascomycota cell cycle; the third is related to morphogenesis. We also compared the method with MatrixReduce and discuss other types of validation and tests. The first network is well known and provides a biological validation test of the method. The two cell cycle case studies, where the gene network size is conserved, demonstrate an effective utility in annotating new species sequences using all the available replicas from model species. The third case, where the gene network size varies among species, shows that the combination of information is less powerful but is still informative. Our methodology is quite general and could be extended to integrate other high-throughput data from model organisms.

Genome Sequences of Oryza Species

KAUST Repository

Kumagai, Masahiko

2018-02-14

This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

Genome Sequences of Oryza Species

KAUST Repository

Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

2018-01-01

This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

A comparative evaluation of sequence classification programs

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Bazinet Adam L

2012-05-01

Full Text Available Abstract Background A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics. Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for ’barcoding genes’ like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis. Results We divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known. Conclusions We found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs.

Blazar Sequence in Fermi Era Liang Chen

Indian Academy of Sciences (India)

Abstract. In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power- high-synchrotron-peaked and ...

Synaptotagmin gene content of the sequenced genomes

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Craxton Molly

2004-07-01

Full Text Available Abstract Background Synaptotagmins exist as a large gene family in mammals. There is much interest in the function of certain family members which act crucially in the regulated synaptic vesicle exocytosis required for efficient neurotransmission. Knowledge of the functions of other family members is relatively poor and the presence of Synaptotagmin genes in plants indicates a role for the family as a whole which is wider than neurotransmission. Identification of the Synaptotagmin genes within completely sequenced genomes can provide the entire Synaptotagmin gene complement of each sequenced organism. Defining the detailed structures of all the Synaptotagmin genes and their encoded products can provide a useful resource for functional studies and a deeper understanding of the evolution of the gene family. The current rapid increase in the number of sequenced genomes from different branches of the tree of life, together with the public deposition of evolutionarily diverse transcript sequences make such studies worthwhile. Results I have compiled a detailed list of the Synaptotagmin genes of Caenorhabditis, Anopheles, Drosophila, Ciona, Danio, Fugu, Mus, Homo, Arabidopsis and Oryza by examining genomic and transcript sequences from public sequence databases together with some transcript sequences obtained by cDNA library screening and RT-PCR. I have compared all of the genes and investigated the relationship between plant Synaptotagmins and their non-Synaptotagmin counterparts. Conclusions I have identified and compared 98 Synaptotagmin genes from 10 sequenced genomes. Detailed comparison of transcript sequences reveals abundant and complex variation in Synaptotagmin gene expression and indicates the presence of Synaptotagmin genes in all animals and land plants. Amino acid sequence comparisons indicate patterns of conservation and diversity in function. Phylogenetic analysis shows the origin of Synaptotagmins in multicellular eukaryotes and their

Unified Deep Learning Architecture for Modeling Biology Sequence.

Science.gov (United States)

Wu, Hongjie; Cao, Chengyuan; Xia, Xiaoyan; Lu, Qiang

2017-10-09

Prediction of the spatial structure or function of biological macromolecules based on their sequence remains an important challenge in bioinformatics. When modeling biological sequences using traditional sequencing models, characteristics, such as long-range interactions between basic units, the complicated and variable output of labeled structures, and the variable length of biological sequences, usually lead to different solutions on a case-by-case basis. This study proposed the use of bidirectional recurrent neural networks based on long short-term memory or a gated recurrent unit to capture long-range interactions by designing the optional reshape operator to adapt to the diversity of the output labels and implementing a training algorithm to support the training of sequence models capable of processing variable-length sequences. Additionally, the merge and pooling operators enhanced the ability to capture short-range interactions between basic units of biological sequences. The proposed deep-learning model and its training algorithm might be capable of solving currently known biological sequence-modeling problems through the use of a unified framework. We validated our model on one of the most difficult biological sequence-modeling problems currently known, with our results indicating the ability of the model to obtain predictions of protein residue interactions that exceeded the accuracy of current popular approaches by 10% based on multiple benchmarks.

Safety Assessment of Advanced Imaging Sequences I: Measurements

DEFF Research Database (Denmark)

Jensen, Jørgen Arendt; Rasmussen, Morten Fischer; Pihl, Michael Johannes

2016-01-01

intensity measurement program. The approach can measure and store data for a full imaging sequence in 3.8 to 8.2 s per spatial position. Based on Ispta, MI, and probe surface temperature, the method gives the ability to determine whether a sequence is within US FDA limits, or alternatively indicate how......A method for rapid measurement of intensities (Ispta), mechanical index (MI), and probe surface temperature for any ultrasound scanning sequence is presented. It uses the scanner’s sampling capability to give an accurate measurement of the whole imaging sequence for all emissions to yield the true...... measurement system (Onda Corporation, Sunnyvale, CA, USA). Four different sequences have been measured: a fixed focus emission, a duplex sequence containing B-mode and flow emissions, a vector flow sequence with B-mode and flow emissions in 17 directions, and finally a synthetic aperture (SA) duplex flow...

New Sequences with Low Correlation and Large Family Size

Science.gov (United States)

Zeng, Fanxin

In direct-sequence code-division multiple-access (DS-CDMA) communication systems and direct-sequence ultra wideband (DS-UWB) radios, sequences with low correlation and large family size are important for reducing multiple access interference (MAI) and accepting more active users, respectively. In this paper, a new collection of families of sequences of length pn-1, which includes three constructions, is proposed. The maximum number of cyclically distinct families without GMW sequences in each construction is φ(pn-1)/n·φ(pm-1)/m, where p is a prime number, n is an even number, and n=2m, and these sequences can be binary or polyphase depending upon choice of the parameter p. In Construction I, there are pn distinct sequences within each family and the new sequences have at most d+2 nontrivial periodic correlation {-pm-1, -1, pm-1, 2pm-1,…,dpm-1}. In Construction II, the new sequences have large family size p2n and possibly take the nontrivial correlation values in {-pm-1, -1, pm-1, 2pm-1,…,(3d-4)pm-1}. In Construction III, the new sequences possess the largest family size p(d-1)n and have at most 2d correlation levels {-pm-1, -1,pm-1, 2pm-1,…,(2d-2)pm-1}. Three constructions are near-optimal with respect to the Welch bound because the values of their Welch-Ratios are moderate, WR_??_d, WR_??_3d-4 and WR_??_2d-2, respectively. Each family in Constructions I, II and III contains a GMW sequence. In addition, Helleseth sequences and Niho sequences are special cases in Constructions I and III, and their restriction conditions to the integers m and n, pm≠2 (mod 3) and n≅0 (mod 4), respectively, are removed in our sequences. Our sequences in Construction III include the sequences with Niho type decimation 3·2m-2, too. Finally, some open questions are pointed out and an example that illustrates the performance of these sequences is given.

SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level.

Science.gov (United States)

Heinke, Florian; Bittrich, Sebastian; Kaiser, Florian; Labudde, Dirk

2016-01-01

To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasing number of available structures in databases or structure models produced by automated modeling frameworks this process requires assistance from tools that allow automated structure visualization. In this paper a web server and its underlying method for generating graphical sequence representations of molecular structures is presented. The method, called SequenceCEROSENE (color encoding of residues obtained by spatial neighborhood embedding), retrieves the sequence of each amino acid or nucleotide chain in a given structure and produces a color coding for each residue based on three-dimensional structure information. From this, color-highlighted sequences are obtained, where residue coloring represent three-dimensional residue locations in the structure. This color encoding thus provides a one-dimensional representation, from which spatial interactions, proximity and relations between residues or entire chains can be deduced quickly and solely from color similarity. Furthermore, additional heteroatoms and chemical compounds bound to the structure, like ligands or coenzymes, are processed and reported as well. To provide free access to SequenceCEROSENE, a web server has been implemented that allows generating color codings for structures deposited in the Protein Data Bank or structure models uploaded by the user. Besides retrieving visualizations in popular graphic formats, underlying raw data can be downloaded as well. In addition, the server provides user interactivity with generated visualizations and the three-dimensional structure in question. Color encoded sequences generated by SequenceCEROSENE can aid to quickly perceive the general characteristics of a structure of interest (or entire sets of complexes), thus supporting the researcher in the initial

Prediction of Protein Structural Classes for Low-Similarity Sequences Based on Consensus Sequence and Segmented PSSM

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Yunyun Liang

2015-01-01

Full Text Available Prediction of protein structural classes for low-similarity sequences is useful for understanding fold patterns, regulation, functions, and interactions of proteins. It is well known that feature extraction is significant to prediction of protein structural class and it mainly uses protein primary sequence, predicted secondary structure sequence, and position-specific scoring matrix (PSSM. Currently, prediction solely based on the PSSM has played a key role in improving the prediction accuracy. In this paper, we propose a novel method called CSP-SegPseP-SegACP by fusing consensus sequence (CS, segmented PsePSSM, and segmented autocovariance transformation (ACT based on PSSM. Three widely used low-similarity datasets (1189, 25PDB, and 640 are adopted in this paper. Then a 700-dimensional (700D feature vector is constructed and the dimension is decreased to 224D by using principal component analysis (PCA. To verify the performance of our method, rigorous jackknife cross-validation tests are performed on 1189, 25PDB, and 640 datasets. Comparison of our results with the existing PSSM-based methods demonstrates that our method achieves the favorable and competitive performance. This will offer an important complementary to other PSSM-based methods for prediction of protein structural classes for low-similarity sequences.

Whole Genome Sequencing of Enterovirus species C Isolates by High-throughput Sequencing: Development of Generic Primers

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Maël Bessaud

2016-08-01

Full Text Available Enteroviruses are among the most common viruses infecting humans and can cause diverse clinical syndromes ranging from minor febrile illness to severe and potentially fatal diseases. Enterovirus species C (EV-C consists of more than 20 types, among which the 3 serotypes of polioviruses, the etiological agents of poliomyelitis, are included. Biodiversity and evolution of EV-C genomes are shaped by frequent recombination events. Therefore, identification and characterization of circulating EV-C strains require the sequencing of different genomic regions.A simple method was developed to sequence quickly the entire genome of EV-C isolates. Four overlapping fragments were produced separately by RT-PCR performed with generic primers. The four amplicons were then pooled and purified prior to be sequenced by high-throughput technique.The method was assessed on a panel of EV-Cs belonging to a wide-range of types. It can be used to determine full-length genome sequences through de novo assembly of thousands of reads. It was also able to discriminate reads from closely related viruses in mixtures.By decreasing the workload compared to classical Sanger-based techniques, this method will serve as a precious tool for sequencing large panels of EV-Cs isolated in cell cultures during environmental surveillance or from patients, including vaccine-derived polioviruses.

FASH: A web application for nucleotides sequence search

Directory of Open Access Journals (Sweden)

Chew Paul

2008-05-01

Full Text Available Abstract FASH (Fourier Alignment Sequence Heuristics is a web application, based on the Fast Fourier Transform, for finding remote homologs within a long nucleic acid sequence. Given a query sequence and a long text-sequence (e.g, the human genome, FASH detects subsequences within the text that are remotely-similar to the query. FASH offers an alternative approach to Blast/Fasta for querying long RNA/DNA sequences. FASH differs from these other approaches in that it does not depend on the existence of contiguous seed-sequences in its initial detection phase. The FASH web server is user friendly and very easy to operate. Availability FASH can be accessed at https://fash.bgu.ac.il:8443/fash/default.jsp (secured website

Whole-genome sequence of the first sequence type 27 Brucella ceti strain isolated from European waters

DEFF Research Database (Denmark)

Duvnjak, Sanja; Spicic, Silvio; Kusar, Darja

2017-01-01

Brucella spp. that cause marine brucellosis are becoming more important, as the disease appears to be more widespread than originally thought. Here, we report a whole and annotated genome sequence of Brucella ceti CRO350, a sequence type 27 strain isolated from a bottlenose dolphin carcass found...

Bunches of random cross-correlated sequences

International Nuclear Information System (INIS)

Maystrenko, A A; Melnik, S S; Pritula, G M; Usatenko, O V

2013-01-01

The statistical properties of random cross-correlated sequences constructed by the convolution method (likewise referred to as the Rice or the inverse Fourier transformation) are examined. We clarify the meaning of the filtering function—the kernel of the convolution operator—and show that it is the value of the cross-correlation function which describes correlations between the initial white noise and constructed correlated sequences. The matrix generalization of this method for constructing a bunch of N cross-correlated sequences is presented. Algorithms for their generation are reduced to solving the problem of decomposition of the Fourier transform of the correlation matrix into a product of two mutually conjugate matrices. Different decompositions are considered. The limits of weak and strong correlations for the one-point probability and pair correlation functions of sequences generated by the method under consideration are studied. Special cases of heavy-tailed distributions of the generated sequences are analyzed. We show that, if the filtering function is rather smooth, the distribution function of generated variables has the Gaussian or Lévy form depending on the analytical properties of the distribution (or characteristic) functions of the initial white noise. Anisotropic properties of statistically homogeneous random sequences related to the asymmetry of a filtering function are revealed and studied. These asymmetry properties are expressed in terms of the third- or fourth-order correlation functions. Several examples of the construction of correlated chains with a predefined correlation matrix are given. (paper)

Towards predicting the encoding capability of MR fingerprinting sequences.

Science.gov (United States)

Sommer, K; Amthor, T; Doneva, M; Koken, P; Meineke, J; Börnert, P

2017-09-01

Sequence optimization and appropriate sequence selection is still an unmet need in magnetic resonance fingerprinting (MRF). The main challenge in MRF sequence design is the lack of an appropriate measure of the sequence's encoding capability. To find such a measure, three different candidates for judging the encoding capability have been investigated: local and global dot-product-based measures judging dictionary entry similarity as well as a Monte Carlo method that evaluates the noise propagation properties of an MRF sequence. Consistency of these measures for different sequence lengths as well as the capability to predict actual sequence performance in both phantom and in vivo measurements was analyzed. While the dot-product-based measures yielded inconsistent results for different sequence lengths, the Monte Carlo method was in a good agreement with phantom experiments. In particular, the Monte Carlo method could accurately predict the performance of different flip angle patterns in actual measurements. The proposed Monte Carlo method provides an appropriate measure of MRF sequence encoding capability and may be used for sequence optimization. Copyright © 2017 Elsevier Inc. All rights reserved.

Sequence memory based on coherent spin-interaction neural networks.

Science.gov (United States)

Xia, Min; Wong, W K; Wang, Zhijie

2014-12-01

Sequence information processing, for instance, the sequence memory, plays an important role on many functions of brain. In the workings of the human brain, the steady-state period is alterable. However, in the existing sequence memory models using heteroassociations, the steady-state period cannot be changed in the sequence recall. In this work, a novel neural network model for sequence memory with controllable steady-state period based on coherent spininteraction is proposed. In the proposed model, neurons fire collectively in a phase-coherent manner, which lets a neuron group respond differently to different patterns and also lets different neuron groups respond differently to one pattern. The simulation results demonstrating the performance of the sequence memory are presented. By introducing a new coherent spin-interaction sequence memory model, the steady-state period can be controlled by dimension parameters and the overlap between the input pattern and the stored patterns. The sequence storage capacity is enlarged by coherent spin interaction compared with the existing sequence memory models. Furthermore, the sequence storage capacity has an exponential relationship to the dimension of the neural network.

SeqCompress: an algorithm for biological sequence compression.

Science.gov (United States)

Sardaraz, Muhammad; Tahir, Muhammad; Ikram, Ataul Aziz; Bajwa, Hassan

2014-10-01

The growth of Next Generation Sequencing technologies presents significant research challenges, specifically to design bioinformatics tools that handle massive amount of data efficiently. Biological sequence data storage cost has become a noticeable proportion of total cost in the generation and analysis. Particularly increase in DNA sequencing rate is significantly outstripping the rate of increase in disk storage capacity, which may go beyond the limit of storage capacity. It is essential to develop algorithms that handle large data sets via better memory management. This article presents a DNA sequence compression algorithm SeqCompress that copes with the space complexity of biological sequences. The algorithm is based on lossless data compression and uses statistical model as well as arithmetic coding to compress DNA sequences. The proposed algorithm is compared with recent specialized compression tools for biological sequences. Experimental results show that proposed algorithm has better compression gain as compared to other existing algorithms. Copyright © 2014 Elsevier Inc. All rights reserved.

SNAD: sequence name annotation-based designer

Directory of Open Access Journals (Sweden)

Gorbalenya Alexander E

2009-08-01

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

Multipliers on Generalized Mixed Norm Sequence Spaces

Directory of Open Access Journals (Sweden)

Oscar Blasco

2014-01-01

Full Text Available Given 1≤p,q≤∞ and sequences of integers (nkk and (nk′k such that nk≤nk′≤nk+1, the generalized mixed norm space ℓℐ(p,q is defined as those sequences (ajj such that ((∑j∈Ik‍|aj|p1/pk∈ℓq where Ik={j∈ℕ0 s.t. nk≤jsequence λ=(λjj to belong to the space of multipliers (ℓℐ(r,s,ℓ(u,v, for different sequences ℐ and of intervals in ℕ0, are determined.

Polynomial sequences generated by infinite Hessenberg matrices

Directory of Open Access Journals (Sweden)

Verde-Star Luis

2017-01-01

Full Text Available We show that an infinite lower Hessenberg matrix generates polynomial sequences that correspond to the rows of infinite lower triangular invertible matrices. Orthogonal polynomial sequences are obtained when the Hessenberg matrix is tridiagonal. We study properties of the polynomial sequences and their corresponding matrices which are related to recurrence relations, companion matrices, matrix similarity, construction algorithms, and generating functions. When the Hessenberg matrix is also Toeplitz the polynomial sequences turn out to be of interpolatory type and we obtain additional results. For example, we show that every nonderogative finite square matrix is similar to a unique Toeplitz-Hessenberg matrix.

High resolution sequence stratigraphy in China

International Nuclear Information System (INIS)

Zhang Shangfeng; Zhang Changmin; Yin Yanshi; Yin Taiju

2008-01-01

Since high resolution sequence stratigraphy was introduced into China by DENG Hong-wen in 1995, it has been experienced two development stages in China which are the beginning stage of theory research and development of theory research and application, and the stage of theoretical maturity and widely application that is going into. It is proved by practices that high resolution sequence stratigraphy plays more and more important roles in the exploration and development of oil and gas in Chinese continental oil-bearing basin and the research field spreads to the exploration of coal mine, uranium mine and other strata deposits. However, the theory of high resolution sequence stratigraphy still has some shortages, it should be improved in many aspects. The authors point out that high resolution sequence stratigraphy should be characterized quantitatively and modelized by computer techniques. (authors)

Characterizing leader sequences of CRISPR loci

DEFF Research Database (Denmark)

Alkhnbashi, Omer; Shah, Shiraz Ali; Garrett, Roger Antony

2016-01-01

The CRISPR-Cas system is an adaptive immune system in many archaea and bacteria, which provides resistance against invading genetic elements. The first phase of CRISPR-Cas immunity is called adaptation, in which small DNA fragments are excised from genetic elements and are inserted into a CRISPR...... array generally adjacent to its so called leader sequence at one end of the array. It has been shown that transcription initiation and adaptation signals of the CRISPR array are located within the leader. However, apart from promoters, there is very little knowledge of sequence or structural motifs...... sequences by focusing on the consensus repeat of the adjacent CRISPR array and weak upstream conservation signals. We applied our tool to the analysis of a comprehensive genomic database and identified several characteristic properties of leader sequences specific to archaea and bacteria, ranging from...

AlignMe—a membrane protein sequence alignment web server

Science.gov (United States)

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

Nucleotide sequence preservation of human mitochondrial DNA

International Nuclear Information System (INIS)

Monnat, R.J. Jr.; Loeb, L.A.

1985-01-01

Recombinant DNA techniques have been used to quantitate the amount of nucleotide sequence divergence in the mitochondrial DNA population of individual normal humans. Mitochondrial DNA was isolated from the peripheral blood lymphocytes of five normal humans and cloned in M13 mp11; 49 kilobases of nucleotide sequence information was obtained from 248 independently isolated clones from the five normal donors. Both between- and within-individual differences were identified. Between-individual differences were identified in approximately = to 1/200 nucleotides. In contrast, only one within-individual difference was identified in 49 kilobases of nucleotide sequence information. This high degree of mitochondrial nucleotide sequence homogeneity in human somatic cells is in marked contrast to the rapid evolutionary divergence of human mitochondrial DNA and suggests the existence of mechanisms for the concerted preservation of mammalian mitochondrial DNA sequences in single organisms

Spreadsheet macros for coloring sequence alignments.

Science.gov (United States)

Haygood, M G

1993-12-01

This article describes a set of Microsoft Excel macros designed to color amino acid and nucleotide sequence alignments for review and preparation of visual aids. The colored alignments can then be modified to emphasize features of interest. Procedures for importing and coloring sequences are described. The macro file adds a new menu to the menu bar containing sequence-related commands to enable users unfamiliar with Excel to use the macros more readily. The macros were designed for use with Macintosh computers but will also run with the DOS version of Excel.

Whole-genome sequencing of veterinary pathogens

DEFF Research Database (Denmark)

Ronco, Troels

-electrophoresis and single-locus sequencing has been widely used to characterize such types of veterinary pathogens. However, DNA sequencing techniques have become fast and cost effective in recent years and whole-genome sequencing data provide a much higher discriminative power and reproducibility than any...... genetic background. This indicates that dairy cows can be natural carriers of S. aureus subtypes that in certain cases lead to CM. A group of isolates that mostly belonged to ST151 carried three pathogenicity islands that were primarily found in this group. The prevalence of resistance genes was generally...

Osteocalcin protein sequences of Neanderthals and modern primates.

Science.gov (United States)

Nielsen-Marsh, Christina M; Richards, Michael P; Hauschka, Peter V; Thomas-Oates, Jane E; Trinkaus, Erik; Pettitt, Paul B; Karavanic, Ivor; Poinar, Hendrik; Collins, Matthew J

2005-03-22

We report here protein sequences of fossil hominids, from two Neanderthals dating to approximately 75,000 years old from Shanidar Cave in Iraq. These sequences, the oldest reported fossil primate protein sequences, are of bone osteocalcin, which was extracted and sequenced by using MALDI-TOF/TOF mass spectrometry. Through a combination of direct sequencing and peptide mass mapping, we determined that Neanderthals have an osteocalcin amino acid sequence that is identical to that of modern humans. We also report complete osteocalcin sequences for chimpanzee (Pan troglodytes) and gorilla (Gorilla gorilla gorilla) and a partial sequence for orangutan (Pongo pygmaeus), all of which are previously unreported. We found that the osteocalcin sequences of Neanderthals, modern human, chimpanzee, and orangutan are unusual among mammals in that the ninth amino acid is proline (Pro-9), whereas most species have hydroxyproline (Hyp-9). Posttranslational hydroxylation of Pro-9 in osteocalcin by prolyl-4-hydroxylase requires adequate concentrations of vitamin C (l-ascorbic acid), molecular O(2), Fe(2+), and 2-oxoglutarate, and also depends on enzyme recognition of the target proline substrate consensus sequence Leu-Gly-Ala-Pro-9-Ala-Pro-Tyr occurring in most mammals. In five species with Pro-9-Val-10, hydroxylation is blocked, whereas in gorilla there is a mixture of Pro-9 and Hyp-9. We suggest that the absence of hydroxylation of Pro-9 in Pan, Pongo, and Homo may reflect response to a selective pressure related to a decline in vitamin C in the diet during omnivorous dietary adaptation, either independently or through the common ancestor of these species.

High-Throughput Block Optical DNA Sequence Identification.

Science.gov (United States)

Sagar, Dodderi Manjunatha; Korshoj, Lee Erik; Hanson, Katrina Bethany; Chowdhury, Partha Pratim; Otoupal, Peter Britton; Chatterjee, Anushree; Nagpal, Prashant

2018-01-01

Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm -1 . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On site DNA barcoding by nanopore sequencing.

Directory of Open Access Journals (Sweden)

Michele Menegon

Full Text Available Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.

Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences | Center for Cancer Research

Science.gov (United States)

A graphical method is presented for displaying how binding proteins and other macromolecules interact with individual bases of nucleotide sequences. Characters representing the sequence are either oriented normally and placed above a line indicating favorable contact, or upside-down and placed below the line indicating unfavorable contact. The positive or negative height of each letter shows the contribution of that base to the average sequence conservation of the binding site, as represented by a sequence logo.

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

DEFF Research Database (Denmark)

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

2005-01-01

sequences (0.66X coverage) from the pig genome. The data are hereby released (NCBI Trace repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project") together with an initial evolutionary analysis. The non-repetitive fraction of the sequences was aligned to the UCSC human...

Next generation sequencing (NGS)technologies and applications

Energy Technology Data Exchange (ETDEWEB)

Vuyisich, Momchilo [Los Alamos National Laboratory

2012-09-11

NGS technology overview: (1) NGS library preparation - Nucleic acids extraction, Sample quality control, RNA conversion to cDNA, Addition of sequencing adapters, Quality control of library; (2) Sequencing - Clonal amplification of library fragments, (except PacBio), Sequencing by synthesis, Data output (reads and quality); and (3) Data analysis - Read mapping, Genome assembly, Gene expression, Operon structure, sRNA discovery, and Epigenetic analyses.

Facies and depositional model of Almada Canyon, Almada Basin, Bahia, Brazil; Facies e modelo deposicional do Canyon de Almada, Bacia de Almada, Bahia

Energy Technology Data Exchange (ETDEWEB)

D' Avila, Roberto Salvador Francisco; Souza Cruz, Carlos Emanoel de; Oliveira Filho, Jose Souto; Jesus, Candida Menezes de; Cesero, Pedro de; Dias Filho, Dorval Carvalho; Lima, Claudio Coelho de; Queiroz, Claudia Lima de; Santos, Saulo Ferreira; Ferreira, Eduardo Araripe [PETROBRAS, Santos, SP (Brazil). Unidade de Negocio de Exploracao]. E-mail: rdavila@petrobras.com.br

2004-11-01

In the continental portion of the Almada Basin outcrops of canyon filling deposits are represented by turbidite channels and associated facies from Urucutuca Formation. The canyon - semi-exhumated - eroded basement and pre-Cenomanian sedimentary rocks. The field study of the outcrops and cores obtained in adjacent perforations lead to the understanding of the facies and processes that controlled the deposition of these channeled turbidite that can be compared to the reservoirs of many oil fields in Brazil. The Almada canyon is a submarine conduct of tectonic origin that was enlarged by the repeated passing of turbidity currents. During the rift phase and the Albian period, compressive events reactivated old N E and N W faults in the basement as trans current fault systems. The continuation of these stresses, from the Cenomanian to the Maastrichtian, developed normal faults that controlled a submarine canyon that connected the continent, where an estuary was formed between the mountains, to the deep marine region of the basin. The canyon has received sediments brought by catastrophic fluvial floods coming from the surrounding mountains, which formed hyperpicnal flows that have evolved as turbidity currents, thus causing erosion of the substrate and carrying a huge volume of sediments to the basin. A part of that load was deposited in the canyon and formed turbidite channels filled by conglomerates, sandstones and shales. These moderately to highly efficient turbidite are intercalated to pro delta pelites and low density turbid plumes deposits, which have mostly been re mobilized as slump and debris flows (chaotic deposits). Pelites were accumulated mainly in the normal fluvial sedimentation phases, when the sandy sediment was retained next to the canyon head and were reworked by the tides on the upper part of the estuary. (author)

Parallel motif extraction from very long sequences

KAUST Repository

Sahli, Majed

2013-01-01

Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

Explaining the harmonic sequence paradox.

Science.gov (United States)

Schmidt, Ulrich; Zimper, Alexander

2012-05-01

According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced. ©2011 The British Psychological Society.

A neurocomputational model of automatic sequence production.

Science.gov (United States)

Helie, Sebastien; Roeder, Jessica L; Vucovich, Lauren; Rünger, Dennis; Ashby, F Gregory

2015-07-01

Most behaviors unfold in time and include a sequence of submovements or cognitive activities. In addition, most behaviors are automatic and repeated daily throughout life. Yet, relatively little is known about the neurobiology of automatic sequence production. Past research suggests a gradual transfer from the associative striatum to the sensorimotor striatum, but a number of more recent studies challenge this role of the BG in automatic sequence production. In this article, we propose a new neurocomputational model of automatic sequence production in which the main role of the BG is to train cortical-cortical connections within the premotor areas that are responsible for automatic sequence production. The new model is used to simulate four different data sets from human and nonhuman animals, including (1) behavioral data (e.g., RTs), (2) electrophysiology data (e.g., single-neuron recordings), (3) macrostructure data (e.g., TMS), and (4) neurological circuit data (e.g., inactivation studies). We conclude with a comparison of the new model with existing models of automatic sequence production and discuss a possible new role for the BG in automaticity and its implication for Parkinson's disease.

Generation of pseudo-random sequences for spread spectrum systems

Science.gov (United States)

Moser, R.; Stover, J.

1985-05-01

The characteristics of pseudo random radio signal sequences (PRS) are explored. The randomness of the PSR is a matter of artificially altering the sequence of binary digits broadcast. Autocorrelations of the two sequences shifted in time, if high, determine if the signals are the same and thus allow for position identification. Cross-correlation can also be calculated between sequences. Correlations closest to zero are obtained with large volume of prime numbers in the sequences. Techniques for selecting optimal and maximal lengths for the sequences are reviewed. If the correlations are near zero in the sequences, then signal channels can accommodate multiple users. Finally, Gold codes are discussed as a technique for maximizing the code lengths.

Special Issue: Next Generation DNA Sequencing

Directory of Open Access Journals (Sweden)

Paul Richardson

2010-10-01

Full Text Available Next Generation Sequencing (NGS refers to technologies that do not rely on traditional dideoxy-nucleotide (Sanger sequencing where labeled DNA fragments are physically resolved by electrophoresis. These new technologies rely on different strategies, but essentially all of them make use of real-time data collection of a base level incorporation event across a massive number of reactions (on the order of millions versus 96 for capillary electrophoresis for instance. The major commercial NGS platforms available to researchers are the 454 Genome Sequencer (Roche, Illumina (formerly Solexa Genome analyzer, the SOLiD system (Applied Biosystems/Life Technologies and the Heliscope (Helicos Corporation. The techniques and different strategies utilized by these platforms are reviewed in a number of the papers in this special issue. These technologies are enabling new applications that take advantage of the massive data produced by this next generation of sequencing instruments. [...

Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing

Science.gov (United States)

Rocher, Solen; Jean, Martine; Castonguay, Yves; Belzile, François

2015-01-01

Genotyping-by-sequencing (GBS) is a relatively low-cost high throughput genotyping technology based on next generation sequencing and is applicable to orphan species with no reference genome. A combination of genome complexity reduction and multiplexing with DNA barcoding provides a simple and affordable way to resolve allelic variation between plant samples or populations. GBS was performed on ApeKI libraries using DNA from 48 genotypes each of two heterogeneous populations of tetraploid alfalfa (Medicago sativa spp. sativa): the synthetic cultivar Apica (ATF0) and a derived population (ATF5) obtained after five cycles of recurrent selection for superior tolerance to freezing (TF). Nearly 400 million reads were obtained from two lanes of an Illumina HiSeq 2000 sequencer and analyzed with the Universal Network-Enabled Analysis Kit (UNEAK) pipeline designed for species with no reference genome. Following the application of whole dataset-level filters, 11,694 single nucleotide polymorphism (SNP) loci were obtained. About 60% had a significant match on the Medicago truncatula syntenic genome. The accuracy of allelic ratios and genotype calls based on GBS data was directly assessed using 454 sequencing on a subset of SNP loci scored in eight plant samples. Sequencing depth in this study was not sufficient for accurate tetraploid allelic dosage, but reliable genotype calls based on diploid allelic dosage were obtained when using additional quality filtering. Principal Component Analysis of SNP loci in plant samples revealed that a small proportion (<5%) of the genetic variability assessed by GBS is able to differentiate ATF0 and ATF5. Our results confirm that analysis of GBS data using UNEAK is a reliable approach for genome-wide discovery of SNP loci in outcrossed polyploids. PMID:26115486

Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences.

Directory of Open Access Journals (Sweden)

Stéphanie Barthe

Full Text Available Simple sequence repeat (SSR markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM. Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR sequences, it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels, and single nucleotide polymorphisms (SNPs observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within

Memory for sequences of events impaired in typical aging

Science.gov (United States)

Allen, Timothy A.; Morris, Andrea M.; Stark, Shauna M.; Fortin, Norbert J.

2015-01-01

Typical aging is associated with diminished episodic memory performance. To improve our understanding of the fundamental mechanisms underlying this age-related memory deficit, we previously developed an integrated, cross-species approach to link converging evidence from human and animal research. This novel approach focuses on the ability to remember sequences of events, an important feature of episodic memory. Unlike existing paradigms, this task is nonspatial, nonverbal, and can be used to isolate different cognitive processes that may be differentially affected in aging. Here, we used this task to make a comprehensive comparison of sequence memory performance between younger (18–22 yr) and older adults (62–86 yr). Specifically, participants viewed repeated sequences of six colored, fractal images and indicated whether each item was presented “in sequence” or “out of sequence.” Several out of sequence probe trials were used to provide a detailed assessment of sequence memory, including: (i) repeating an item from earlier in the sequence (“Repeats”; e.g., ABADEF), (ii) skipping ahead in the sequence (“Skips”; e.g., ABDDEF), and (iii) inserting an item from a different sequence into the same ordinal position (“Ordinal Transfers”; e.g., AB3DEF). We found that older adults performed as well as younger controls when tested on well-known and predictable sequences, but were severely impaired when tested using novel sequences. Importantly, overall sequence memory performance in older adults steadily declined with age, a decline not detected with other measures (RAVLT or BPS-O). We further characterized this deficit by showing that performance of older adults was severely impaired on specific probe trials that required detailed knowledge of the sequence (Skips and Ordinal Transfers), and was associated with a shift in their underlying mnemonic representation of the sequences. Collectively, these findings provide unambiguous evidence that the

The nucleotide sequences of two leghemoglobin genes from soybean

DEFF Research Database (Denmark)

Wiborg, O; Hyldig-Nielsen, J J; Jensen, E O

1982-01-01

We present the complete nucleotide sequences of two leghemoglobin genes isolated from soybean DNA. Both genes contain three intervening sequences in identical positions. Comparison of the coding sequences with known amino-acid sequences of soybean leghemoglobins suggest that the two genes...

Multiple tag labeling method for DNA sequencing

Science.gov (United States)

Mathies, R.A.; Huang, X.C.; Quesada, M.A.

1995-07-25

A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

Exome Sequencing in Suspected Monogenic Dyslipidemias

Science.gov (United States)

Stitziel, Nathan O.; Peloso, Gina M.; Abifadel, Marianne; Cefalu, Angelo B.; Fouchier, Sigrid; Motazacker, M. Mahdi; Tada, Hayato; Larach, Daniel B.; Awan, Zuhier; Haller, Jorge F.; Pullinger, Clive R.; Varret, Mathilde; Rabès, Jean-Pierre; Noto, Davide; Tarugi, Patrizia; Kawashiri, Masa-aki; Nohara, Atsushi; Yamagishi, Masakazu; Risman, Marjorie; Deo, Rahul; Ruel, Isabelle; Shendure, Jay; Nickerson, Deborah A.; Wilson, James G.; Rich, Stephen S.; Gupta, Namrata; Farlow, Deborah N.; Neale, Benjamin M.; Daly, Mark J.; Kane, John P.; Freeman, Mason W.; Genest, Jacques; Rader, Daniel J.; Mabuchi, Hiroshi; Kastelein, John J.P.; Hovingh, G. Kees; Averna, Maurizio R.; Gabriel, Stacey; Boileau, Catherine; Kathiresan, Sekar

2015-01-01

Background Exome sequencing is a promising tool for gene mapping in Mendelian disorders. We utilized this technique in an attempt to identify novel genes underlying monogenic dyslipidemias. Methods and Results We performed exome sequencing on 213 selected family members from 41 kindreds with suspected Mendelian inheritance of extreme levels of low-density lipoprotein (LDL) cholesterol (after candidate gene sequencing excluded known genetic causes for high LDL cholesterol families) or high-density lipoprotein (HDL) cholesterol. We used standard analytic approaches to identify candidate variants and also assigned a polygenic score to each individual in order to account for their burden of common genetic variants known to influence lipid levels. In nine families, we identified likely pathogenic variants in known lipid genes (ABCA1, APOB, APOE, LDLR, LIPA, and PCSK9); however, we were unable to identify obvious genetic etiologies in the remaining 32 families despite follow-up analyses. We identified three factors that limited novel gene discovery: (1) imperfect sequencing coverage across the exome hid potentially causal variants; (2) large numbers of shared rare alleles within families obfuscated causal variant identification; and (3) individuals from 15% of families carried a significant burden of common lipid-related alleles, suggesting complex inheritance can masquerade as monogenic disease. Conclusions We identified the genetic basis of disease in nine of 41 families; however, none of these represented novel gene discoveries. Our results highlight the promise and limitations of exome sequencing as a discovery technique in suspected monogenic dyslipidemias. Considering the confounders identified may inform the design of future exome sequencing studies. PMID:25632026

A programmable method for massively parallel targeted sequencing

Science.gov (United States)

Hopmans, Erik S.; Natsoulis, Georges; Bell, John M.; Grimes, Susan M.; Sieh, Weiva; Ji, Hanlee P.

2014-01-01

We have developed a targeted resequencing approach referred to as Oligonucleotide-Selective Sequencing. In this study, we report a series of significant improvements and novel applications of this method whereby the surface of a sequencing flow cell is modified in situ to capture specific genomic regions of interest from a sample and then sequenced. These improvements include a fully automated targeted sequencing platform through the use of a standard Illumina cBot fluidics station. Targeting optimization increased the yield of total on-target sequencing data 2-fold compared to the previous iteration, while simultaneously increasing the percentage of reads that could be mapped to the human genome. The described assays cover up to 1421 genes with a total coverage of 5.5 Megabases (Mb). We demonstrate a 10-fold abundance uniformity of greater than 90% in 1 log distance from the median and a targeting rate of up to 95%. We also sequenced continuous genomic loci up to 1.5 Mb while simultaneously genotyping SNPs and genes. Variants with low minor allele fraction were sensitively detected at levels of 5%. Finally, we determined the exact breakpoint sequence of cancer rearrangements. Overall, this approach has high performance for selective sequencing of genome targets, configuration flexibility and variant calling accuracy. PMID:24782526

NeSSM: a Next-generation Sequencing Simulator for Metagenomics.

Directory of Open Access Journals (Sweden)

Ben Jia

Full Text Available BACKGROUND: Metagenomics can reveal the vast majority of microbes that have been missed by traditional cultivation-based methods. Due to its extremely wide range of application areas, fast metagenome sequencing simulation systems with high fidelity are in great demand to facilitate the development and comparison of metagenomics analysis tools. RESULTS: We present here a customizable metagenome simulation system: NeSSM (Next-generation Sequencing Simulator for Metagenomics. Combining complete genomes currently available, a community composition table, and sequencing parameters, it can simulate metagenome sequencing better than existing systems. Sequencing error models based on the explicit distribution of errors at each base and sequencing coverage bias are incorporated in the simulation. In order to improve the fidelity of simulation, tools are provided by NeSSM to estimate the sequencing error models, sequencing coverage bias and the community composition directly from existing metagenome sequencing data. Currently, NeSSM supports single-end and pair-end sequencing for both 454 and Illumina platforms. In addition, a GPU (graphics processing units version of NeSSM is also developed to accelerate the simulation. By comparing the simulated sequencing data from NeSSM with experimental metagenome sequencing data, we have demonstrated that NeSSM performs better in many aspects than existing popular metagenome simulators, such as MetaSim, GemSIM and Grinder. The GPU version of NeSSM is more than one-order of magnitude faster than MetaSim. CONCLUSIONS: NeSSM is a fast simulation system for high-throughput metagenome sequencing. It can be helpful to develop tools and evaluate strategies for metagenomics analysis and it's freely available for academic users at http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php.

Highly multiplexed targeted DNA sequencing from single nuclei.

Science.gov (United States)

Leung, Marco L; Wang, Yong; Kim, Charissa; Gao, Ruli; Jiang, Jerry; Sei, Emi; Navin, Nicholas E

2016-02-01

Single-cell DNA sequencing methods are challenged by poor physical coverage, high technical error rates and low throughput. To address these issues, we developed a single-cell DNA sequencing protocol that combines flow-sorting of single nuclei, time-limited multiple-displacement amplification (MDA), low-input library preparation, DNA barcoding, targeted capture and next-generation sequencing (NGS). This approach represents a major improvement over our previous single nucleus sequencing (SNS) Nature Protocols paper in terms of generating higher-coverage data (>90%), thereby enabling the detection of genome-wide variants in single mammalian cells at base-pair resolution. Furthermore, by pooling 48-96 single-cell libraries together for targeted capture, this approach can be used to sequence many single-cell libraries in parallel in a single reaction. This protocol greatly reduces the cost of single-cell DNA sequencing, and it can be completed in 5-6 d by advanced users. This single-cell DNA sequencing protocol has broad applications for studying rare cells and complex populations in diverse fields of biological research and medicine.

Insights from 20 years of bacterial genome sequencing

DEFF Research Database (Denmark)

Land, Miriam; Hauser, Loren; Jun, Se-Ran

2015-01-01

Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along...... the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative...... genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling...

The diploid genome sequence of an Asian individual

DEFF Research Database (Denmark)

Wang, Jun; Wang, Wei; Li, Ruiqiang

2008-01-01

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we...... used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP...... identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J...

Massively parallel sequencing of forensic STRs

DEFF Research Database (Denmark)

Parson, Walther; Ballard, David; Budowle, Bruce

2016-01-01

The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that...

Thread extraction for polyadic instruction sequences

NARCIS (Netherlands)

Bergstra, J.; Middelburg, C.

2011-01-01

In this paper, we study the phenomenon that instruction sequences are split into fragments which somehow produce a joint behaviour. In order to bring this phenomenon better into the picture, we formalize a simple mechanism by which several instruction sequence fragments can produce a joint

What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research

OpenAIRE

Bräutigam, Andrea; Gowik, Udo

2010-01-01

Next generation sequencing (NGS) technologies have opened fascinating opportunities for the analysis of plants with and without a sequenced genome on a genomic scale. During the last few years, NGS methods have become widely available and cost effective. They can be applied to a wide variety of biological questions, from the sequencing of complete eukaryotic genomes and transcriptomes, to the genome-scale analysis of DNA-protein interactions. In this review, we focus on the use of NGS for pla...

Enhanced learning of natural visual sequences in newborn chicks.

Science.gov (United States)

Wood, Justin N; Prasad, Aditya; Goldman, Jason G; Wood, Samantha M W

2016-07-01

To what extent are newborn brains designed to operate over natural visual input? To address this question, we used a high-throughput controlled-rearing method to examine whether newborn chicks (Gallus gallus) show enhanced learning of natural visual sequences at the onset of vision. We took the same set of images and grouped them into either natural sequences (i.e., sequences showing different viewpoints of the same real-world object) or unnatural sequences (i.e., sequences showing different images of different real-world objects). When raised in virtual worlds containing natural sequences, newborn chicks developed the ability to recognize familiar images of objects. Conversely, when raised in virtual worlds containing unnatural sequences, newborn chicks' object recognition abilities were severely impaired. In fact, the majority of the chicks raised with the unnatural sequences failed to recognize familiar images of objects despite acquiring over 100 h of visual experience with those images. Thus, newborn chicks show enhanced learning of natural visual sequences at the onset of vision. These results indicate that newborn brains are designed to operate over natural visual input.

CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

Energy Technology Data Exchange (ETDEWEB)

G.E. Ragan; P. Mecheret; D. Dexheimer

2005-04-14

The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis.