Genome classification by gene distribution: an overlapping subspace clustering approach.

BMC Evolutionary Biology
Jason LiSen-Lin Tang

Abstract

Genomes of lower organisms have been observed with a large amount of horizontal gene transfers, which cause difficulties in their evolutionary study. Bacteriophage genomes are a typical example. One recent approach that addresses this problem is the unsupervised clustering of genomes based on gene order and genome position, which helps to reveal species relationships that may not be apparent from traditional phylogenetic methods. We propose the use of an overlapping subspace clustering algorithm for such genome classification problems. The advantage of subspace clustering over traditional clustering is that it can associate clusters with gene arrangement patterns, preserving genomic information in the clusters produced. Additionally, overlapping capability is desirable for the discovery of multiple conserved patterns within a single genome, such as those acquired from different species via horizontal gene transfers. The proposed method involves a novel strategy to vectorize genomes based on their gene distribution. A number of existing subspace clustering and biclustering algorithms were evaluated to identify the best framework upon which to develop our algorithm; we extended a generic subspace clustering algorithm called HARP ...Continue Reading

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Citations

Feb 15, 2011·Journal of Bacteriology·David M KristensenArcady Mushegian
Oct 12, 2012·BMC Genomics·Jason J GillRy Young
Nov 13, 2012·Computers & Operations Research·Harun PirimCetin Yüceer
Jan 1, 2018·Applied Network Science·Giulia CesariJuan A Nepomuceno

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