Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
Nucleic Acids Res. 2018 Jan 4;46(D1):D213-D217. doi: 10.1093/nar/gkx997.
The APPRIS database (http://appris-tools.org) uses protein structural and functional features and information from cross-species conservation to annotate splice isoforms in protein-coding genes. APPRIS selects a single protein isoform, the 'principal' isoform, as the reference for each gene based on these annotations. A single main splice isoform reflects the biological reality for most protein coding genes and APPRIS principal isoforms are the best predictors of these main proteins isoforms. Here, we present the updates to the database, new developments that include the addition of three new species (chimpanzee, Drosophila melangaster and Caenorhabditis elegans), the expansion of APPRIS to cover the RefSeq gene set and the UniProtKB proteome for six species and refinements in the core methods that make up the annotation pipeline. In addition APPRIS now provides a measure of reliability for individual principal isoforms and updates with each release of the GENCODE/Ensembl and RefSeq reference sets. The individual GENCODE/Ensembl, RefSeq and UniProtKB reference gene sets for six organisms have been merged to produce common sets of splice variants.
APPRIS 数据库（http://appris-tools.org）使用蛋白质结构和功能特征以及跨物种保守信息来注释蛋白质编码基因中的剪接异构体。APPRIS 根据这些注释，选择单个蛋白质异构体，即“主要”异构体，作为每个基因的参考。大多数蛋白质编码基因的单个主要剪接异构体反映了生物学现实，而 APPRIS 主要异构体是这些主要蛋白质异构体的最佳预测因子。在这里，我们介绍了数据库的更新，包括三个新物种（黑猩猩、果蝇和秀丽隐杆线虫）的添加，APPRIS 扩展到涵盖 RefSeq 基因集和六个物种的 UniProtKB 蛋白质组，以及构成注释管道的核心方法的改进。此外，APPRIS 现在为每个主要异构体提供了可靠性度量，并在 GENCODE/Ensembl 和 RefSeq 参考集的每次更新中进行更新。已经合并了六个生物体的单个 GENCODE/Ensembl、RefSeq 和 UniProtKB 参考基因集，以生成常见的剪接变体集。
