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Bioinformatics. 2012 Dec 15;28(24):3316-7. doi: 10.1093/bioinformatics/bts599. Epub 2012 Oct 9.

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

Author information

1
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA. redwards@mail.sdsu.edu

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.

PMID:
23047562
PMCID:
PMC3519453
DOI:
10.1093/bioinformatics/bts599
[Indexed for MEDLINE]
Free PMC Article

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