MersV1, Main, Exploration, bibRecord, 002486

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.

Identifieur interne : 002486 ( Main/Exploration ); précédent : 002485; suivant : 002487

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.

Auteurs : Guillaume Marçais [États-Unis] ; Carl Kingsford

Source :

Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2011.

RBID : pubmed:21217122

Descripteurs français

KwdFr :
- Algorithmes, Alignement de séquences, Analyse de séquence d'ADN (), Animaux, Biologie informatique (), Génome, Humains, Logiciel, Séquence nucléotidique.
MESH :
- Algorithmes, Alignement de séquences, Analyse de séquence d'ADN, Animaux, Biologie informatique, Génome, Humains, Logiciel, Séquence nucléotidique.

English descriptors

KwdEn :
- Algorithms, Animals, Base Sequence, Computational Biology (methods), Genome, Humans, Sequence Alignment, Sequence Analysis, DNA (methods), Software.
MESH :
- methods : Computational Biology, Sequence Analysis, DNA.
- Algorithms, Animals, Base Sequence, Genome, Humans, Sequence Alignment, Software.

Abstract

Counting the number of occurrences of every k-mer (substring of length k) in a long string is a central subproblem in many applications, including genome assembly, error correction of sequencing reads, fast multiple sequence alignment and repeat detection. Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be processed during a genome project to grow rapidly, and has rendered current k-mer counting tools too slow and memory intensive. At the same time, large multicore computers have become commonplace in research facilities allowing for a new parallel computational paradigm.

DOI: 10.1093/bioinformatics/btr011
PubMed: 21217122

Affiliations:

Le document en format XML

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<term>Animals</term>
<term>Base Sequence</term>
<term>Genome</term>
<term>Humans</term>
<term>Sequence Alignment</term>
<term>Software</term>
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<term>Alignement de séquences</term>
<term>Analyse de séquence d'ADN</term>
<term>Animaux</term>
<term>Biologie informatique</term>
<term>Génome</term>
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<front><div type="abstract" xml:lang="en">Counting the number of occurrences of every k-mer (substring of length k) in a long string is a central subproblem in many applications, including genome assembly, error correction of sequencing reads, fast multiple sequence alignment and repeat detection. Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be processed during a genome project to grow rapidly, and has rendered current k-mer counting tools too slow and memory intensive. At the same time, large multicore computers have become commonplace in research facilities allowing for a new parallel computational paradigm.</div>
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Serveur d'exploration MERS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

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