ISU Electrical and Computer Engineering Archives

A Unified Model for Multi-genome Synteny and Gene Cluster Inference

Yang, Xiao and Srinivas, Aluru (2009) A Unified Model for Multi-genome Synteny and Gene Cluster Inference. Publisher UNSPECIFIED.

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Inferring evolutionarily related genomic regions among multiple genomes is an important and well-studied problem in comparative genomics. Existing models fail to fully capture the various evolutionary events and typically model multiple genome comparisons through what can be inferred from constituent pairwise comparisons. In this paper, we present a unified model for gene cluster and synteny detection that simultaneously captures multiple genomic regions related through genomic inversions, gene duplications, insertions and losses, which may occur in one or multiple genomic sequences. We then present an algorithm to deduce all multi-syntenies within a given set of genomic sequences, and demonstrate its effectiveness by identifying gene clusters across two microbial genomes and multi-syntenies among the 12 chromosomes of the rice genome. Our method achieves better sensitivity and specificity in identifying documented operons when compared with HomologyTeams model.

EPrint Type:Technical Report
Uncontrolled Keywords:comparative genomics, gene teams, gene cluster, synteny, homology
Subjects:Computer Engineering > SOFTWARE SYSTEMS > Computational Biology and Computational Science
ID Code:494
Identification Number:Identification Number UNSPECIFIED
Deposited By:Xiao Yang
Deposited On:02 June 2009

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