Real time metagenomics: using k-mers to annotate metagenomes.
Identifieur interne : 001D42 ( PubMed/Corpus ); précédent : 001D41; suivant : 001D43Real time metagenomics: using k-mers to annotate metagenomes.
Auteurs : Robert A. Edwards ; Robert Olson ; Terry Disz ; Gordon D. Pusch ; Veronika Vonstein ; Rick Stevens ; Ross OverbeekSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2012.
English descriptors
- KwdEn :
- MESH :
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
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pubmed:23047562Le document en format XML
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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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