COG database update: focus on microbial diversity, model organisms, and widespread pathogens
COG database update: focus on microbial diversity, model organisms, and widespread pathogens
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DOI：
10.1093/nar/gkaa1018
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发表时间：
2021-01-08
影响因子：
14.9
通讯作者：
Koonin, Eugene, V
中科院分区：
文献类型：
--
作者：
Galperin, Michael Y.;Wolf, Yuri, I;Koonin, Eugene, V
直向同源基因簇 (COG) 数据库，也称为蛋白质直向同源群簇，创建于 1997 年，并经历了几轮更新，最近一次是在 2014 年。当前更新可在 https://www.ncbi.nlm.nih.gov/research/COG 上获取，大幅扩展了数据库的范围，包括 1187 种细菌和 122 种古细菌的完整基因组，通常，每个属只有一个基因组。此外，当前版本的 COG 还包括以下新功能： (i) 最近弃用的 NCBI 编码蛋白的基因索引 (gi) 编号已替换为稳定的 RefSeq 或 GenBank\ENA\DDBJ 编码序列 (CDS) 登录号； (ii) 更新了超过 200 个新表征的蛋白质家族的 COG 注释，以及相应的参考文献和 PDB 链接（如果有）； (iii) 添加了按途径和功能系统分组的 COG 列表； (iv) 包括 266 个新的 COG，涉及 CRISPR-Cas 免疫、厚壁菌门中的孢子形成和蓝细菌中的光合作用的蛋白质； (v) 除了 FTP 之外，数据库还以网页形式提供。当前版本包括 4877 个 COG。未来的计划包括通过添加古菌 COG (arCOG)、拆分包含多个旁系同源物的 COG 以及继续细化 COG 注释来进一步扩展 COG 集合。
The Clusters of Orthologous Genes (COG) database, also referred to as the Clusters of Orthologous Groups of proteins, was created in 1997 and went through several rounds of updates, most recently, in 2014. The current update, available at https: //www.ncbi.nlm.nih.gov/ research/COG, substantially expands the scope of the database to include complete genomes of 1187 bacteria and 122 archaea, typically, with a single genome per genus. In addition, the current version of the COGs includes the following new features: (i) the recently deprecated NCBI's gene index (gi) numbers for the encoded proteins are replaced with stable RefSeq or GenBank\ENA\DDBJ coding sequence (CDS) accession numbers; (ii) COG annotations are updated for >200 newly characterized protein families with corresponding references and PDB links, where available; (iii) lists of COGs grouped by pathways and functional systems are added; (iv) 266 new COGs for proteins involved in CRISPR-Cas immunity, sporulation in Firmicutes and photosynthesis in cyanobacteria are included; and (v) the database is made available as a web page, in addition to FTP. The current release includes 4877 COGs. Future plans include further expansion of the COG collection by adding archaeal COGs (arCOGs), splitting the COGs containing multiple paralogs, and continued refinement of COG annotations.