European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. doi: 10.1093/nar/gkr1060. Epub 2011 Nov 16.
Orthologous relationships form the basis of most comparative genomic and metagenomic studies and are essential for proper phylogenetic and functional analyses. The third version of the eggNOG database (http://eggnog.embl.de) contains non-supervised orthologous groups constructed from 1133 organisms, doubling the number of genes with orthology assignment compared to eggNOG v2. The new release is the result of a number of improvements and expansions: (i) the underlying homology searches are now based on the SIMAP database; (ii) the orthologous groups have been extended to 41 levels of selected taxonomic ranges enabling much more fine-grained orthology assignments; and (iii) the newly designed web page is considerably faster with more functionality. In total, eggNOG v3 contains 721,801 orthologous groups, encompassing a total of 4,396,591 genes. Additionally, we updated 4873 and 4850 original COGs and KOGs, respectively, to include all 1133 organisms. At the universal level, covering all three domains of life, 101,208 orthologous groups are available, while the others are applicable at 40 more limited taxonomic ranges. Each group is amended by multiple sequence alignments and maximum-likelihood trees and broad functional descriptions are provided for 450,904 orthologous groups (62.5%).
同源关系是大多数比较基因组学和宏基因组学研究的基础，对于正确的系统发育和功能分析至关重要。eggNOG 数据库的第三个版本（http://eggnog.embl.de）包含了从 1133 个生物体中构建的无监督同源物组，与 eggNOG v2 相比，同源基因的数量增加了一倍。新版本是许多改进和扩展的结果：（i）基础同源搜索现在基于 SIMAP 数据库；（ii）同源物组已扩展到 41 个选定的分类范围级别，从而实现了更细粒度的同源物分配；（iii）新设计的网页速度更快，功能更多。总的来说，eggNOG v3 包含 721,801 个同源物组，共包含 4,396,591 个基因。此外，我们更新了 4873 个和 4850 个原始 COG 和 KOG，分别包含所有 1133 个生物体。在普遍水平上，涵盖了生命的三个领域，有 101,208 个同源物组可用，而其他的则适用于 40 个更有限的分类范围。每个组都经过了多次序列比对和最大似然树的修正，并为 450,904 个同源物组（62.5%）提供了广泛的功能描述。
