Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups.
Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups.
复制标题
使用orthomcl将蛋白质分配给Orthomcl-DB组或将蛋白质组群集分为新的直系同源组。
DOI：
10.1002/0471250953.bi0612s35
复制
发表时间：
2011-09
影响因子：
--
通讯作者：
Stoeckert, Christian J Jr
中科院分区：
文献类型：
--
作者：
Fischer, Steve;Brunk, Brian P;Chen, Feng;Gao, Xin;Harb, Omar S;Iodice, John B;Shanmugam, Dhanasekaran;Roos, David S;Stoeckert, Christian J Jr
OrthoMCL是一种基于序列相似性将蛋白质分组为同源群的算法。OrthoMCL- db是一个公共数据库，允许用户浏览和查看使用OrthoMCL算法预先计算的同源组。该数据库的第4版包含从88个真核生物基因组、16个古细菌基因组和34个细菌基因组中获得的1,270,853个蛋白质中聚集的116,536个同源群。OrthoMCL-DB的未来版本将包括更多的蛋白质组，因为更多的基因组被测序。在这里，我们描述了如何使用OrthoMCL系统提供的两种不同方法将感兴趣的蛋白质分组到同源簇中。OrthoMCL-DB网站有一个上传和分组一组蛋白质序列的工具，通常代表一个蛋白质组。该方法将上传的蛋白质映射到OrthoMCL-DB中的现有组。另外，如果你需要对一组基因组中的蛋白质进行分组，你可以下载、安装并运行独立的OrthoMCL软件。
OrthoMCL is an algorithm for grouping proteins into ortholog groups based on their sequence similarity. OrthoMCL-DB is a public database that allows users to browse and view ortholog groups that were pre-computed using the OrthoMCL algorithm. Version 4 of this database contained 116,536 ortholog groups clustered from 1,270,853 proteins obtained from 88 eukaryotic genomes, 16 archaeal genomes and 34 bacterial genomes. Future versions of OrthoMCL-DB will include more proteomes as more genomes are sequenced. Here, we describe how you can group your proteins of interest into ortholog clusters using two different means provided by the OrthoMCL system. The OrthoMCL-DB website has a tool for uploading and grouping a set of protein sequences, typically representing a proteome. This method maps the uploaded proteins to existing groups in OrthoMCL-DB. Alternatively, if you have proteins from a set of genomes that need to be grouped, you can download, install and run the standalone OrthoMCL software.