OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs.
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs.
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DOI：
10.1093/nar/gky1053
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发表时间：
2019-01-08
影响因子：
14.9
通讯作者：
Zdobnov EM
中科院分区：
文献类型：
--
作者：
Kriventseva EV;Kuznetsov D;Tegenfeldt F;Manni M;Dias R;Simão FA;Zdobnov EM
OrthoDB（www.orthodb.org）提供了直系同源物的进化和功能注释。本次更新的特点是资源覆盖范围的大幅扩大，对1271种真核生物、6013种原核生物和6488种病毒的基因组多样性进行了采样。这些包括448后生动物，117植物，549真菌，148原生生物，5609细菌和404古细菌基因组之间的推定直系同源物，挑选最好的测序和注释的代表每个物种或操作分类单位。OrthoDB依赖于同源性级别的分层概念，为更密切相关的物种提供更精细的基因同源性。由于直向同源物是最有可能保留其祖先基因功能的候选者，因此OrthoDB旨在缩小有关基因功能的假设并进行比较进化研究。可选的注册用户会话允许在线BUSCO评估基因集的完整性，并将上传的数据映射到OrthoDB，以进一步交互式探索相关注释和生成比较图表。基因组学数据的加速扩展继续增加有价值的信息，OrthoDB致力于提供最广泛的物种直向同源物，以及广泛整理可用的功能注释和计算进化注释。数据可以通过与UniProt和Ensembl兼容的REST API或SPARQL RDF在线浏览、下载或评估。
OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up of the resource coverage, sampling the genomic diversity of 1271 eukaryotes, 6013 prokaryotes and 6488 viruses. These include putative orthologs among 448 metazoan, 117 plant, 549 fungal, 148 protist, 5609 bacterial, and 404 archaeal genomes, picking up the best sequenced and annotated representatives for each species or operational taxonomic unit. OrthoDB relies on a concept of hierarchy of levels-of-orthology to enable more finely resolved gene orthologies for more closely related species. Since orthologs are the most likely candidates to retain functions of their ancestor gene, OrthoDB is aimed at narrowing down hypotheses about gene functions and enabling comparative evolutionary studies. Optional registered-user sessions allow on-line BUSCO assessments of gene set completeness and mapping of the uploaded data to OrthoDB to enable further interactive exploration of related annotations and generation of comparative charts. The accelerating expansion of genomics data continues to add valuable information, and OrthoDB strives to provide orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations and to compute evolutionary annotations. The data can be browsed online, downloaded or assessed via REST API or SPARQL RDF compatible with both UniProt and Ensembl.
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Orthodb：真核直系同源物的分层目录。
影响因子：
14.9
作者：
Kriventseva, Evgenia V.;Rahman, Nazim;Espinosa, Octavio;Zdobnov, Evgeny M.
通讯作者：
Zdobnov, Evgeny M.
影响因子：
14.9
作者：
Federhen S
通讯作者：
Federhen S
影响因子：
14.9
作者：
Sonnhammer EL;Östlund G
通讯作者：
Östlund G
影响因子：
14.9
作者：
Huerta-Cepas J;Capella-Gutiérrez S;Pryszcz LP;Marcet-Houben M;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
5.8
作者：
Simao, Felipe A.;Waterhouse, Robert M.;Zdobnov, Evgeny M.
通讯作者：
Zdobnov, Evgeny M.