Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes

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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. Crown Copyright 2011.2011This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/ licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. © Crown Copyright 2011.

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Li, G., Ma, Q., Mao, X., Yin, Y., Zhu, X., & Xu, Y. (2011). Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes. Nucleic Acids Research, 39(22). https://doi.org/10.1093/nar/gkr766

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