MersV1, PubMed, Checkpoint, bibRecord, 001C41

Real time metagenomics: using k-mers to annotate metagenomes.

Identifieur interne : 001C41 ( PubMed/Checkpoint ); précédent : 001C40; suivant : 001C42

Real time metagenomics: using k-mers to annotate metagenomes.

Auteurs : Robert A. Edwards [États-Unis] ; Robert Olson ; Terry Disz ; Gordon D. Pusch ; Veronika Vonstein ; Rick Stevens ; Ross Overbeek

Source :

Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2012.

RBID : pubmed:23047562

Descripteurs français

KwdFr :
- Algorithmes, Analyse de séquence d'ADN, Annotation de séquence moléculaire, Métagénome, Métagénomique ().
MESH :
- Algorithmes, Analyse de séquence d'ADN, Annotation de séquence moléculaire, Métagénome, Métagénomique.

English descriptors

KwdEn :
- Algorithms, Metagenome, Metagenomics (methods), Molecular Sequence Annotation, Sequence Analysis, DNA.
MESH :
- methods : Metagenomics.
- Algorithms, Metagenome, Molecular Sequence Annotation, Sequence Analysis, DNA.

Abstract

Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.

DOI: 10.1093/bioinformatics/bts599
PubMed: 23047562

Affiliations:

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Le document en format XML

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<author><name sortKey="Pusch, Gordon D" sort="Pusch, Gordon D" uniqKey="Pusch G" first="Gordon D" last="Pusch">Gordon D. Pusch</name>
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<author><name sortKey="Vonstein, Veronika" sort="Vonstein, Veronika" uniqKey="Vonstein V" first="Veronika" last="Vonstein">Veronika Vonstein</name>
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<author><name sortKey="Stevens, Rick" sort="Stevens, Rick" uniqKey="Stevens R" first="Rick" last="Stevens">Rick Stevens</name>
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<front><div type="abstract" xml:lang="en">Annotation of metagenomes involves comparing the individual sequence reads with a database of known sequences and assigning a unique function to each read. This is a time-consuming task that is computationally intensive (though not computationally complex). Here we present a novel approach to annotate metagenomes using unique k-mer oligopeptide sequences from 7 to 12 amino acids long. We demonstrate that k-mer-based annotations are faster and approach the sensitivity and precision of blastx-based annotations without loosing accuracy. A last-common ancestor approach was also developed to describe the members of the community.</div>
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<Reference><Citation>Nucleic Acids Res. 2012 Jul;40(12):e94</Citation>
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Real time metagenomics: using k-mers to annotate metagenomes.

Real time metagenomics: using k-mers to annotate metagenomes.

Source :

Descripteurs français

English descriptors

Abstract

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

Links to Exploration step

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