Microbial genome analysis: the COG approach
Microbial genome analysis: the COG approach
复制标题
DOI：
10.1093/bib/bbx117
复制
发表时间：
2019-07-01
影响因子：
9.5
通讯作者：
Koonin, Eugene V.
中科院分区：
文献类型：
--
作者：
Galperin, Michael Y.;Kristensen, David M.;Koonin, Eugene V.
在过去的20年里，COG数据库一直是微生物基因组注释和比较基因组学的热门工具。COG最初是为了蛋白质家族的进化分类而创建的，除了测序基因组的直接功能注释外，还用于以下任务：（i）相关生物体组中基因组注释的统一;（ii）完整微生物基因组中缺失和/或未检测到的基因的鉴定;（iii）完整微生物基因组中缺失和/或未检测到的基因的鉴定。（iii）分析基因组邻域，在许多情况下允许预测新的功能系统;（iv）分析代谢途径和预测酶的替代形式;（v）通过COG功能类别比较生物体;和（vi）结构和功能表征的目标的优先次序。在这里，我们回顾了COG方法的原理，并讨论了其在微生物基因组分析中的主要优点和缺点。
For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis.