eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
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DOI：
10.1093/nar/gky1085
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发表时间：
2019-01-08
影响因子：
14.9
通讯作者：
Bork, Peer
中科院分区：
文献类型：
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作者：
Huerta-Cepas, Jaime;Szklarczyk, Damian;Bork, Peer
EggNOG 是一个直系同源关系、基因进化历史和功能注释的公共数据库。在这里，我们推出了 5.0 版本，对基础基因组集进行了重大更新，已扩展到来自 25 038 个基因组的 4445 种代表性细菌和 168 种古细菌，以及 477 种真核生物和 2502 个病毒蛋白质组，这些蛋白质组经过多样性选择并按基因组质量进行过滤。总共计算了分布在 379 个分类级别的 440 万个直系同源群 (OG) 及其相关序列比对、系统发育、HMM 模型和功能描述符。预先计算的进化分析提供了每个 OG 内重复/物种形成事件的细粒度分辨率。我们的基准测试表明，尽管基因组数量增加了一倍，直系同源分配和功能注释的质量（80% 覆盖率）仍然保持不变，在这次更新中没有发生重大变化。最后，我们改进了 EggNOG 在线服务，以实现自定义基因组学或宏基因组学数据集的快速功能注释和同源预测。所有预先计算的数据均可公开下载或通过 API 查询：http://eggnog.embl.de
eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 eukaryotic organisms and 2502 viral proteomes that were selected for diversity and filtered by genome quality. In total, 4.4M orthologous groups (OGs) distributed across 379 taxonomic levels were computed together with their associated sequence alignments, phylogenies, HMM models and functional descriptors. Precomputed evolutionary analysis provides fine-grained resolution of duplication/speciation events within each OG. Our benchmarks show that, despite doubling the amount of genomes, the quality of orthology assignments and functional annotations (80% coverage) has persisted without significant changes across this update. Finally, we improved eggNOG online services for fast functional annotation and orthology prediction of custom genomics or metagenomics datasets. All precomputed data are publicly available for downloading or via API queries at http://eggnog.embl.de