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

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

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Abstract

Inferring evolutionarily related genomic regions is an important and well-studied problem in comparative genomics, which has been modeled as synteny detection or gene clusters detection. Existing methods well capture a subset of evolutionary events and typically model syntenies or gene clusters involving multiple regions through constituent pairs. In this paper, we present a unified model for synteny and gene cluster 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 term these evoluionarily related regions as multirelated- regions (abbreviated MRR), and then present an algorithm to deduce all MRRs within a given set of genomic sequences, and demonstrate its effectiveness by identifying gene clusters across two microbial genomes and 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:496
Identification Number:Identification Number UNSPECIFIED
Deposited By:Xiao Yang
Deposited On:20 July 2009

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