Hsu Chih-Hao, Zhang Yu, Hardison Ross C, Green Eric D, Miller Webb
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA.
J Comput Biol. 2010 Sep;17(9):1281-97. doi: 10.1089/cmb.2010.0103.
Gene conversion events are often overlooked in analyses of genome evolution. In a conversion event, an interval of DNA sequence (not necessarily containing a gene) overwrites a highly similar sequence. The event creates relationships among genomic intervals that can confound attempts to identify orthologs and to transfer functional annotation between genomes. Here we examine 1,616,329 paralogous pairs of mouse genomic intervals, and detect conversion events in about 7.5% of them. Properties of the putative gene conversions are analyzed, such as the lengths of the paralogous pairs and the spacing between their sources and targets. Our approach is illustrated using conversion events in primate CCL gene clusters. Source code for our program is included in the 3SEQ_2D package, which is freely available at www.bx.psu.edu/miller_lab/ .
基因转换事件在基因组进化分析中常常被忽视。在一次转换事件中，一段DNA序列区间（不一定包含一个基因）会覆盖一段高度相似的序列。该事件在基因组区间之间建立了关系，这可能会干扰识别直系同源基因以及在基因组之间转移功能注释的尝试。在这里，我们检查了1616329对小鼠基因组区间的旁系同源对，并在其中约7.5%的对中检测到了转换事件。我们分析了推定的基因转换的特性，例如旁系同源对的长度以及它们的源和目标之间的间距。我们使用灵长类CCL基因簇中的转换事件来说明我们的方法。我们程序的源代码包含在3SEQ_2D软件包中，该软件包可在www.bx.psu.edu/miller_lab/ 上免费获取。
