Publisher Correction: Optimal compressed representation of high throughput sequence data via light assembly

This paper proposed a way of two-level parallel alignment based on sequence parallel vectorization with GPU acceleration on the Fermi architecture, which integrates sequence parallel vectorization, parallel k-means clustering approximate alignment and parallel Smith-Waterman algorithm. The method converts sequence alignment into vector alignment by first. Then it uses k-means alignment to divide sequences into several groups and reduce the size of sequence data. The expected accurate alignment result is achieved using parallel Smith-Waterman algorithm. The high-throughput mouse T-cell receptor (TCR) sequences were used to validate the proposed method. Under the same hardware condition, comparing to serial Smith-Waterman algorithm and CUDASW++2.0 algorithm, our method is the most efficient alignment algorithm with high alignment accuracy.

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Comprehensive pathogen detection in sera of Kawasaki disease patients by high-throughput sequencing: a retrospective exploratory study

BMC Pediatrics ◽

10.1186/s12887-020-02380-7 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Yuka Torii ◽

Kazuhiro Horiba ◽

Satoshi Hayano ◽

Taichi Kato ◽

Takako Suzuki ◽

...

Keyword(s):

Kawasaki Disease ◽

High Throughput ◽

High Throughput Sequencing ◽

Sequence Data ◽

Early Stage ◽

Rna Virus ◽

Systemic Vasculitis ◽

Human Herpesvirus ◽

Acute Stage ◽

Serum Samples

Abstract Background Kawasaki disease (KD) is an idiopathic systemic vasculitis that predominantly damages coronary arteries in children. Various pathogens have been investigated as triggers for KD, but no definitive causative pathogen has been determined. As KD is diagnosed by symptoms, several days are needed for diagnosis. Therefore, at the time of diagnosis of KD, the pathogen of the trigger may already be diminished. The aim of this study was to explore comprehensive pathogens in the sera at the acute stage of KD using high-throughput sequencing (HTS). Methods Sera of 12 patients at an extremely early stage of KD and 12 controls were investigated. DNA and RNA sequences were read separately using HTS. Sequence data were imported into the home-brew meta-genomic analysis pipeline, PATHDET, to identify the pathogen sequences. Results No RNA virus reads were detected in any KD case except for that of equine infectious anemia, which is known as a contaminant of commercial reverse transcriptase. Concerning DNA viruses, human herpesvirus 6B (HHV-6B, two cases) and Anelloviridae (eight cases) were detected among KD cases as well as controls. Multiple bacterial reads were obtained from KD and controls. Bacteria of the genera Acinetobacter, Pseudomonas, Delfita, Roseomonas, and Rhodocyclaceae appeared to be more common in KD sera than in the controls. Conclusion No single pathogen was identified in serum samples of patients at the acute phase of KD. With multiple bacteria detected in the serum samples, it is difficult to exclude the possibility of contamination; however, it is possible that these bacteria might stimulate the immune system and induce KD.

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High-Throughput Crystallization Pipeline at the Crystallography Core Facility of the Institut Pasteur

Molecules ◽

10.3390/molecules24244451 ◽

2019 ◽

Vol 24 (24) ◽

pp. 4451 ◽

Cited By ~ 6

Author(s):

Patrick Weber ◽

Cédric Pissis ◽

Rafael Navaza ◽

Ariel E. Mechaly ◽

Frederick Saul ◽

...

Keyword(s):

High Throughput ◽

Sequence Data ◽

Data Bank ◽

Whole Genome Sequence ◽

Whole Genome ◽

X Ray Diffraction ◽

Sequencing Technology ◽

X Ray ◽

Set Up ◽

General User

The availability of whole-genome sequence data, made possible by significant advances in DNA sequencing technology, led to the emergence of structural genomics projects in the late 1990s. These projects not only significantly increased the number of 3D structures deposited in the Protein Data Bank in the last two decades, but also influenced present crystallographic strategies by introducing automation and high-throughput approaches in the structure-determination pipeline. Today, dedicated crystallization facilities, many of which are open to the general user community, routinely set up and track thousands of crystallization screening trials per day. Here, we review the current methods for high-throughput crystallization and procedures to obtain crystals suitable for X-ray diffraction studies, and we describe the crystallization pipeline implemented in the medium-scale crystallography platform at the Institut Pasteur (Paris) as an example.

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Toward the development of a gene index to the human genome: an assessment of the nature of high-throughput EST sequence data.

Genome Research ◽

10.1101/gr.6.9.829 ◽

1996 ◽

Vol 6 (9) ◽

pp. 829-845 ◽

Cited By ~ 65

Author(s):

J S Aaronson ◽

B Eckman ◽

R A Blevins ◽

J A Borkowski ◽

J Myerson ◽

...

Keyword(s):

Human Genome ◽

High Throughput ◽

Sequence Data ◽

Est Sequence ◽

Gene Index

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Evidence for Transcriptome-wide RNA Editing Among Sus scrofa PRE-1 SINE Elements

10.1101/096321 ◽

2017 ◽

Author(s):

Scott A. Funkhouser ◽

Juan P. Steibel ◽

Ronald O. Bates ◽

Nancy E. Raney ◽

Darius Schenk ◽

...

Keyword(s):

Genetic Variation ◽

Transcriptional Regulation ◽

Rna Editing ◽

High Throughput ◽

Sus Scrofa ◽

Sequence Data ◽

Rna Sequences ◽

Editing Event ◽

Coding Regions ◽

Dna And Rna

AbstractBackgroundRNA editing by ADAR (adenosine deaminase acting on RNA) proteins is a form of transcriptional regulation that is widespread among humans and other primates. Based on high-throughput scans used to identify putative RNA editing sites, ADAR appears to catalyze a substantial number of adenosine to inosine transitions within repetitive regions of the primate transcriptome, thereby dramatically enhancing genetic variation beyond what is encoded in the genome.ResultsHere, we demonstrate the editing potential of the pig transcriptome by utilizing DNA and RNA sequence data from the same pig. We identified a total of 8550 mismatches between DNA and RNA sequences across three tissues, with 75% of these exhibiting an A-to-G (DNA to RNA) discrepancy, indicative of a canonical ADAR-catalyzed RNA editing event. When we consider only mismatches within repetitive regions of the genome, the A-to-G percentage increases to 94%, with the majority of these located within the swine specific SINE retrotransposon PRE-1. We also observe evidence of A-to-G editing within coding regions that were previously verified in primates.ConclusionsThus, our high-throughput evidence suggests that pervasive RNA editing by ADAR can exist outside of the primate lineage to dramatically enhance genetic variation in pigs.

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