General Information
| Description | Using k-mers to annotate metagenomes |
| Homepage | http://edwards.sdsu.edu/rtmg |
Publications
Real Time Metagenomics: Using k-mers to annotate metagenomes
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.
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