Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes.
Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes.
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序列相似性和功能关联信息的整合可以克服细菌基因组直系图谱中的内在问题
DOI：
10.1093/nar/gkr766
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发表时间：
2011-12
影响因子：
14.9
通讯作者：
Xu Y
中科院分区：
文献类型：
--
作者：
Li G;Ma Q;Mao X;Yin Y;Zhu X;Xu Y
现有的直向同源基因定位方法存在两个普遍问题：（i）当基于系统发育分析时，它们在计算上太慢，并且它们的结果难以解释用于自动化大规模应用;或者（ii）当基于序列相似性信息时，由于缺乏可靠的基础，它们在处理涉及水平基因转移和基因融合的复杂情况时太容易出错。我们提出了一种新的算法，全局优化策略（GOST），通过结合序列相似性和上下文（工作伙伴）的信息，使用组合优化框架的orthopathic基因定位。GOST的基因组规模的应用显示出实质性的改进，由三个流行的序列相似性为基础的同源性映射程序的预测。我们的分析表明，当同源性映射涉及基因融合和水平基因转移时，我们的算法克服了基于序列相似性的方法所面临的固有问题。我们的程序运行效率最有效的序列相似性为基础的算法在公共领域。GOST可在http://csbl.bmb.uga.edu/~maqin/GOST上免费下载。
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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影响因子：
4.3
作者：
Altenhoff, Adrian M.;Dessimoz, Christophe
通讯作者：
Dessimoz, Christophe
影响因子：
14.9
作者：
Yu C;Zavaljevski N;Desai V;Reifman J
通讯作者：
Reifman J
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM
影响因子：
14.9
作者：
Marchler-Bauer A;Lu S;Anderson JB;Chitsaz F;Derbyshire MK;DeWeese-Scott C;Fong JH;Geer LY;Geer RC;Gonzales NR;Gwadz M;Hurwitz DI;Jackson JD;Ke Z;Lanczycki CJ;Lu F;Marchler GH;Mullokandov M;Omelchenko MV;Robertson CL;Song JS;Thanki N;Yamashita RA;Zhang D;Zhang N;Zheng C;Bryant SH
通讯作者：
Bryant SH
影响因子：
3.7
作者：
Chen F;Mackey AJ;Vermunt JK;Roos DS
通讯作者：
Roos DS