Peptide markers of aminoacyl tRNA synthetases facilitate taxa counting in metagenomic data.

ABSTRACT:

Background

Taxa counting is a major problem faced by analysis of metagenomic data. The most popular method relies on analysis of 16S rRNA sequences, but some studies employ also protein based analyses. It would be advantageous to have a method that is applicable directly to short sequences, of the kind extracted from samples in modern metagenomic research. This is achieved by the technique proposed here.

Results

We employ specific peptides, deduced from aminoacyl tRNA synthetases, as markers for the occurrence of single genes in data. Sequences carrying these markers are aligned and compared with each other to provide a lower limit for taxa counts in metagenomic data. The method is compared with 16S rRNA searches on a set of known genomes. The taxa counting problem is analyz

SUBMITTER: Persi E 

PROVIDER: S-EPMC3319421 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature