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

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...

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Detalles Bibliográficos
Autores principales: Li, Guojun, Ma, Qin, Mao, Xizeng, Yin, Yanbin, Zhu, Xiaoran, Xu, Ying
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239196/
https://www.ncbi.nlm.nih.gov/pubmed/21965536
http://dx.doi.org/10.1093/nar/gkr766
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author Li, Guojun
Ma, Qin
Mao, Xizeng
Yin, Yanbin
Zhu, Xiaoran
Xu, Ying
author_facet Li, Guojun
Ma, Qin
Mao, Xizeng
Yin, Yanbin
Zhu, Xiaoran
Xu, Ying
author_sort Li, Guojun
collection PubMed
description 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.
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spelling pubmed-32391962011-12-16 Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes Li, Guojun Ma, Qin Mao, Xizeng Yin, Yanbin Zhu, Xiaoran Xu, Ying Nucleic Acids Res Methods Online 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. Oxford University Press 2011-12 2011-09-29 /pmc/articles/PMC3239196/ /pubmed/21965536 http://dx.doi.org/10.1093/nar/gkr766 Text en © Crown Copyright 2011. http://creativecommons.org/licenses/by-nc/3.0 This 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.
spellingShingle Methods Online
Li, Guojun
Ma, Qin
Mao, Xizeng
Yin, Yanbin
Zhu, Xiaoran
Xu, Ying
Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes
title Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes
title_full Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes
title_fullStr Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes
title_full_unstemmed Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes
title_short Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes
title_sort integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3239196/
https://www.ncbi.nlm.nih.gov/pubmed/21965536
http://dx.doi.org/10.1093/nar/gkr766
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