Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes.
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes.
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DOI：
10.1093/nar/gky1013
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发表时间：
2019-01-08
影响因子：
14.9
通讯作者：
Finn RD
中科院分区：
文献类型：
--
作者：
Richardson LJ;Rawlings ND;Salazar GA;Almeida A;Haft DR;Ducq G;Sutton GG;Finn RD
蛋白质功能的自动注释通常应用于新测序的基因组。虽然这提供了对生物体功能蛋白库的细粒度视图，但蛋白质通常以协调的方式起作用，例如在通路或多聚体复合物中。基因组属性（gp）将这些功能实体定义为一系列步骤，最初由tigrfam或Pfam条目描述。为了增加覆盖范围，我们已经将gp迁移为利用InterPro条目的伙伴资源。引入了GPs特定版本的发布后，我们通过GitHub存储库提供软件和数据，并开发了一个新的GPs web界面（可在https://www.ebi.ac.uk/interpro/genomeproperties上获得）。除了探索1286个gp中的每一个，该网站还包含预先计算的具有代表性的蛋白质组的gp；这些结果可用于通过交互式查看器对GPs系统发育进行分析。用户可以将新数据上传到查看器，以便与预先计算的结果进行比较。在过去的一年中，我们增加了约700个新的gp，增加了真核生物系统的覆盖范围，并通过从相关资源自动生成gp增加了一般覆盖范围。所有数据都可以通过网站和GitHub存储库免费获得。
Automatic annotation of protein function is routinely applied to newly sequenced genomes. While this provides a fine-grained view of an organism's functional protein repertoire, proteins, more commonly function in a coordinated manner, such as in pathways or multimeric complexes. Genome Properties (GPs) define such functional entities as a series of steps, originally described by either TIGRFAMs or Pfam entries. To increase the scope of coverage, we have migrated GPs to function as a companion resource utilizing InterPro entries. Having introduced GPs-specific versioned releases, we provide software and data via a GitHub repository, and have developed a new web interface to GPs (available at https://www.ebi.ac.uk/interpro/genomeproperties). In addition to exploring each of the 1286 GPs, the website contains GPs pre-calculated for a representative set of proteomes; these results can be used to profile GPs phylogenetically via an interactive viewer. Users can upload novel data to the viewer for comparison with the pre-calculated results. Over the last year, we have added ∼700 new GPs, increasing the coverage of eukaryotic systems, as well as increasing general coverage through automatic generation of GPs from related resources. All data are freely available via the website and the GitHub repository.
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影响因子：
14.9
作者：
Haft DH;Selengut JD;Richter RA;Harkins D;Basu MK;Beck E
通讯作者：
Beck E
影响因子：
14.9
作者：
Caspi R;Billington R;Ferrer L;Foerster H;Fulcher CA;Keseler IM;Kothari A;Krummenacker M;Latendresse M;Mueller LA;Ong Q;Paley S;Subhraveti P;Weaver DS;Karp PD
通讯作者：
Karp PD
影响因子：
14.9
作者：
Wattam AR;Davis JJ;Assaf R;Boisvert S;Brettin T;Bun C;Conrad N;Dietrich EM;Disz T;Gabbard JL;Gerdes S;Henry CS;Kenyon RW;Machi D;Mao C;Nordberg EK;Olsen GJ;Murphy-Olson DE;Olson R;Overbeek R;Parrello B;Pusch GD;Shukla M;Vonstein V;Warren A;Xia F;Yoo H;Stevens RL
通讯作者：
Stevens RL
影响因子：
14.9
作者：
Rawlings ND;Barrett AJ;Finn R
通讯作者：
Finn R
影响因子：
28.3
作者：
Parks, Donovan H.;Rinke, Christian;Tyson, Gene W.
通讯作者：
Tyson, Gene W.