A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.

ABSTRACT: Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. Among the computational tools recently developed for metagenomic sequence analysis, binning tools attempt to classify the sequences in a metagenomic dataset into different bins (i.e., species), based on various DNA composition patterns (e.g., the tetramer frequencies) of various genomes. Composition-based binning methods, however, cannot be used to classify very short fragments, because of the substantial variation of DNA composition patterns within a single genome. We developed a novel approach (AbundanceBin) for metagenomics binning by utilizing the different abundances of species living in the same environment. AbundanceBin is an application of the Lander-Waterman

SUBMITTER: Wu YW 

PROVIDER: S-EPMC3123841 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature