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.
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