Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.

ABSTRACT: Metagenomics projects collect DNA from uncharacterized environments that may contain thousands of species per sample. One main challenge facing metagenomic analysis is phylogenetic classification of raw sequence reads into groups representing the same or similar taxa, a prerequisite for genome assembly and for analyzing the biological diversity of a sample. New sequencing technologies have made metagenomics easier, by making sequencing faster, and more difficult, by producing shorter reads than previous technologies. Classifying sequences from reads as short as 100 base pairs has until now been relatively inaccurate, requiring researchers to use older, long-read technologies. We present Phymm, a classifier for metagenomic data, that has been trained on 539 complete, curated genomes and can

SUBMITTER: Brady A 

PROVIDER: S-EPMC2762791 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature