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Real Time Metagenomics: Using k -mers to annotate metagenomes

2012; Oxford University Press; Volume: 28; Issue: 24 Linguagem: Inglês

10.1093/bioinformatics/bts599

1367-4811

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

Machine Learning in Bioinformatics

Abstract Summary: 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 http://edwards.sdsu.edu/rtmg. In addition, code to access the annotation servers is available for download from http://www.theseed.org/. FIGfams and k-mers are available for download from ftp://ftp.theseed.org/FIGfams/. Contact: redwards@mail.sdsu.edu Supplementary information: Supplementary data are available at Bioinformatics online.