RAIphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles.

ABSTRACT:

Background

Computational analysis of metagenomes requires the taxonomical assignment of the genome contigs assembled from DNA reads of environmental samples. Because of the diverse nature of microbiomes, the length of the assemblies obtained can vary between a few hundred bp to a few hundred Kbp. Current taxonomic classification algorithms provide accurate classification for long contigs or for short fragments from organisms that have close relatives with annotated genomes. These are significant limitations for metagenome analysis because of the complexity of microbiomes and the paucity of existing annotated genomes.

Results

We propose a robust taxonomic classification method, RAIphy, that uses a novel sequence similarity metric with iterative refinement of taxonomic models

SUBMITTER: Nalbantoglu OU 

PROVIDER: S-EPMC3038895 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature