Revanna Kashi Vishwanath, Krishnakumar Vivek, Dong Qunfeng
Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA.
Bioinformatics. 2009 Apr 1;25(7):956-7. doi: 10.1093/bioinformatics/btp078. Epub 2009 Feb 9.
Investigating the conservation of gene clusters across multiple genomes has become a standard practice in the era of comparative genomics. However, all existing software and databases rely heavily on pre-computation to identify homologous genes by genome-wide comparisons. Such pre-computing strategies lack accuracy and updating the data is computationally intensive. Since most molecular biologists are often interested only in a small cluster of genes, catering to this need, we have developed a web-based software system that allows users to upload a list of genes, perform dynamic search against the genomes of their choices and interactively visualize the gene cluster conservation using a novel multi-genome browser. Our approach avoids expensive genome-wide pre-computing and allows users to dynamically change the search criteria to fit their genes of interest. Our system can be customized for any genome sequences. We have applied it to both prokaryotic and eukaryotic genomes to illustrate its usability.
Our software is freely available at http://cgcv.cgb.indiana.edu/cgi-bin/index.cgi.
在比较基因组学时代，研究多个基因组中基因簇的保守性已成为一种标准做法。然而，所有现有的软件和数据库都严重依赖预计算，通过全基因组比较来识别同源基因。这种预计算策略缺乏准确性，并且更新数据的计算量很大。由于大多数分子生物学家通常只对一小部分基因簇感兴趣，为满足这一需求，我们开发了一个基于网络的软件系统，该系统允许用户上传基因列表，对他们选择的基因组进行动态搜索，并使用一种新颖的多基因组浏览器交互式地可视化基因簇的保守性。我们的方法避免了昂贵的全基因组预计算，并允许用户动态更改搜索标准以适应他们感兴趣的基因。我们的系统可以针对任何基因组序列进行定制。我们已将其应用于原核生物和真核生物基因组以说明其可用性。
