Rapid identification of high-confidence taxonomic assignments for metagenomic data.

ABSTRACT: Determining the taxonomic lineage of DNA sequences is an important step in metagenomic analysis. Short DNA fragments from next-generation sequencing projects and microbes that lack close relatives in reference sequenced genome databases pose significant problems to taxonomic attribution methods. Our new classification algorithm, RITA (Rapid Identification of Taxonomic Assignments), uses the agreement between composition and homology to accurately classify sequences as short as 50 nt in length by assigning them to different classification groups with varying degrees of confidence. RITA is much faster than the hybrid PhymmBL approach when comparable homology search algorithms are used, and achieves slightly better accuracy than PhymmBL on an artificial metagenome. RITA can also incorporate p

SUBMITTER: MacDonald NJ 

PROVIDER: S-EPMC3413139 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature