Computational clustering for viral reference proteomes
Computational clustering for viral reference proteomes
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DOI：
10.1093/bioinformatics/btw110
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发表时间：
2016-07-01
期刊：
影响因子：
5.8
通讯作者：
Wu, Cathy H.
中科院分区：
文献类型：
--
作者：
Chen, Chuming;Huang, Hongzhan;Wu, Cathy H.
动机：大量冗余测序基因组阻碍了蛋白质分析和功能注释的努力。由于病毒的分类学尚未统一定义，病毒蛋白质组在这方面提出了特殊的挑战。根据蛋白质组水平上蛋白质的相似性对病毒进行分组，可以针对潜在的分类命名异常进行标准化。结果：我们提出了病毒参考蛋白质组（病毒 RP），它是根据 UniProtKB 中的完整病毒蛋白质组计算得出的。提供了基于蛋白质组相似性簇中 95%、75%、55%、35% 和 15% 共同成员的病毒 RP。我们的计算病毒 RP 与 UniProt 策展人选择的参考蛋白质组的比较表明，这两个集合是一致且互补的。此外，每个病毒 RP 代表一组与病毒或宿主分类学一致的病毒蛋白质组。我们提供病毒 RP 蛋白序列的 BLASTP 搜索和 FTP 下载，以及浏览器以促进病毒 RP 的可视化。
Motivation: The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies.Results: We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95, 75, 55, 35 and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt's curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs.