Real Time Metagenomics: Using k-mers to annotate metagenomes

Robert A. Edwards, Robert Olson, Terry Disz, Gordon D. Pusch, Veronika Vonstein, Rick Stevens, Ross Overbeek

Research output: Contribution to journalArticlepeer-review

34 Citations (Scopus)
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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.Availability and implementation: This open-source application was implemented in Perl and can be accessed via a user-friendly website at In addition, code to access the annotation servers is available for download from FIGfams and k-mers are available for download from

Original languageEnglish
Pages (from-to)3316-3317
Number of pages2
Issue number24
Publication statusPublished - Dec 2012
Externally publishedYes

Bibliographical note

© The Author 2012. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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