Journal article

Binning sequences using very sparse labels within a metagenome

Chon-Kit Kenneth Chan, Arthur L Hsu, Saman K Halgamuge, Sen-Lin Tang

BMC BIOINFORMATICS | BMC | Published : 2008

Abstract

BACKGROUND: In metagenomic studies, a process called binning is necessary to assign contigs that belong to multiple species to their respective phylogenetic groups. Most of the current methods of binning, such as BLAST, k-mer and PhyloPythia, involve assigning sequence fragments by comparing sequence similarity or sequence composition with already-sequenced genomes that are still far from comprehensive. We propose a semi-supervised seeding method for binning that does not depend on knowledge of completed genomes. Instead, it extracts the flanking sequences of highly conserved 16S rRNA from the metagenome and uses them as seeds (labels) to assign other reads based on their compositional simil..

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University of Melbourne Researchers