European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
J. Craig Venter Institute (JCVI), 9605 Medical Center Drive, Suite 150, Rockville, MD 20850, USA.
Nucleic Acids Res. 2019 Jan 8;47(D1):D564-D572. doi: 10.1093/nar/gky1013.
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.
自动注释蛋白质功能通常应用于新测序的基因组。虽然这提供了生物体功能蛋白质组的细粒度视图，但蛋白质通常以协调的方式发挥作用，例如在途径或多聚体复合物中。基因组特性 (GP) 将这些功能实体定义为一系列步骤，最初由 TIGRFAMs 或 Pfam 条目描述。为了增加覆盖范围，我们已将 GP 迁移为利用 InterPro 条目作为辅助资源。引入 GP 特定版本后，我们通过 GitHub 存储库提供软件和数据，并开发了一个新的 GP 网络界面（可在 https://www.ebi.ac.uk/interpro/genomeproperties 上访问）。除了探索 1286 个 GP 中的每一个之外，该网站还包含为一组代表性蛋白质组预先计算的 GP；这些结果可通过交互式查看器用于通过系统发育分析 GP。用户可以将新数据上传到查看器中，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，提高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 来提高总体覆盖范围。所有数据均可通过网站和 GitHub 存储库免费获得。
