eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.
复制标题
DOI：
10.1093/nar/gkr1060
复制
发表时间：
2012-01
影响因子：
14.9
通讯作者：
Bork P
中科院分区：
文献类型：
--
作者：
Powell S;Szklarczyk D;Trachana K;Roth A;Kuhn M;Muller J;Arnold R;Rattei T;Letunic I;Doerks T;Jensen LJ;von Mering C;Bork P
直系亲属关系构成了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）包含从1133个生物体构建的非监督的直向组，与eggNOG v2相比，具有直向分配的基因的数量加倍。新版本是若干改进和扩展的结果：（i）基本同源性搜索现在基于SIMAP数据库;（ii）同源性组已扩展到选定分类范围的41个级别，从而能够进行更精细的同源性分配;（iii）新设计的网页速度快得多，功能更多。总的来说，eggNOG v3包含721 801个正向同源群，总共包含4 396 591个基因。此外，我们分别更新了4873和4850个原始COG和KOG，以包括所有1133种微生物。在普遍层面上，涵盖所有三个领域的生活，101 208 orthopathic组，而其他人适用于40个更有限的分类范围。每个组是由多个序列比对和最大似然树和广泛的功能描述，提供了450 904 orthopathic组（62.5%）。
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%).
登录
查看更多内容
ProGMap：蛋白质直系同源的集成注释资源。
影响因子：
14.9
作者：
Kuzniar, Arnold;Lin, Ke;He, Ying;Nijveen, Harm;Pongor, Sandor;Leunissen, Jack A. M.
通讯作者：
Leunissen, Jack A. M.
影响因子：
12.3
作者：
Milinkovitch MC;Helaers R;Depiereux E;Tzika AC;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
5.5
作者：
Makarova KS;Sorokin AV;Novichkov PS;Wolf YI;Koonin EV
通讯作者：
Koonin EV
影响因子：
4.3
作者：
Altenhoff, Adrian M.;Dessimoz, Christophe
通讯作者：
Dessimoz, Christophe
影响因子：
14.9
作者：
Kuhn M;Szklarczyk D;Franceschini A;Campillos M;von Mering C;Jensen LJ;Beyer A;Bork P
通讯作者：
Bork P