Ivliev Alexander E, Sergeeva Marina G
Department of Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia.
J Bioinform Comput Biol. 2008 Aug;6(4):811-24. doi: 10.1142/s0219720008003692.
The identification of orthologs to a set of known genes is often the starting point for evolutionary studies focused on gene families of interest. To date, the existing orthology detection tools (COG, InParanoid, OrthoMCL, etc.) are aimed at genome-wide ortholog identification and lack flexibility for the purposes of case studies. We developed a program OrthoFocus, which employs an extended reciprocal best hit approach to quickly search for orthologs in a pair of genomes. A group of paralogs from the input genome is used as the start for the forward search and the criterion for the reverse search, which allows handling many-to-one and many-to-many relationships. By pairwise comparison of genomes with the input species genome, OrthoFocus enables quick identification of orthologs in multiple genomes and generates a multiple alignment of orthologs so that it can further be used in phylogenetic analysis. The program is available at http://www.lipidomics.ru/.
鉴定与一组已知基因的直系同源物通常是针对感兴趣的基因家族开展进化研究的起点。迄今为止，现有的直系同源物检测工具（COG、InParanoid、OrthoMCL等）旨在进行全基因组直系同源物鉴定，对于案例研究目的而言缺乏灵活性。我们开发了一个程序OrthoFocus，它采用扩展的相互最佳比对方法在一对基因组中快速搜索直系同源物。来自输入基因组的一组旁系同源物被用作正向搜索的起点和反向搜索的标准，这使得能够处理多对一和多对多关系。通过将基因组与输入物种基因组进行成对比较，OrthoFocus能够快速鉴定多个基因组中的直系同源物，并生成直系同源物的多序列比对，以便进一步用于系统发育分析。该程序可在http://www.lipidomics.ru/获取。
