title: Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes.
abstract: Existing methods for orthologous gene mapping suffer from two general problems: (i) they are computationally too slow and their results are difficult to interpret for automated large-scale applications when based on phylogenetic analyses; or (ii) they are too prone to making mistakes in dealing with complex situations involving horizontal gene transfers and gene fusion due to the lack of a sound basis when based on sequence similarity information. We present a novel algorithm, Global Optimization Strategy (GOST), for orthologous gene mapping through combining sequence similarity and contextual (working partners) information, using a combinatorial optimization framework. Genome-scale applications of GOST show substantial improvements over the predictions by three popular sequence similarity-based orthology mapping programs. Our analysis indicates that our algorithm overcomes the intrinsic issues faced by sequence similarity-based methods, when orthology mapping involves gene fusions and horizontal gene transfers. Our program runs as efficiently as the most efficient sequence similarity-based algorithm in the public domain. GOST is freely downloadable at http://csbl.bmb.uga.edu/~maqin/GOST.
authors.affiliation: Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA.
authors.forename: Guojun
authors.initials: G
authors.lastname: Li
authors.forename: Qin
authors.initials: Q
authors.lastname: Ma
authors.forename: Xizeng
authors.initials: X
authors.lastname: Mao
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Yin
authors.forename: Xiaoran
authors.initials: X
authors.lastname: Zhu
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D004269:DNA, Bacterial / Q000737:chemistry; D004798:Enzymes / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D050939:Gene Fusion; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D004269:DNA, Bacterial; D004798:Enzymes