FAIRsharing record for: PGDBj Ortholog Database

This FAIRsharing record describes: The PGDBj Ortholog Database, created under the auspices of the Plant Genome Database Japan (PGDBj), contains information about orthologous genes in plants based on their corresponding amino acid sequence similarity. By placing PGDBj Ortholog Database as a 'hub' within a suite of resources and databases, the aim is to make reciprocal links between databases containing information about various organisms. Users can find orthologs in different subsets of organisms by searching the database using either amino acid information or keywords. The PGDBj 'amino acid sequence DB' contains 500,000 amino acid sequences from 20 plant species classified in Viridiplantae. The PGDBj Ortholog Database provides gene cluster information based on amino acid sequence similarity. Over 500,000 amino acid sequences of 20 Viridiplantae species were subjected to reciprocal BLAST searches and clustered. Sequences from plant genome DBs (e.g. TAIR10 and RAP-DB) were also included in the cluster with a direct link to the original DB. To provide outgroups in the Viridiplantae comparative analyses, ortholog data sets derived from Cyanobacteria and Deuterostomia are also being analyzed.

本FAIRsharing记录介绍的是：由日本植物基因组数据库（Plant Genome Database Japan，简称PGDBj）支持创建的PGDBj直系同源基因数据库（PGDBj Ortholog Database），基于对应氨基酸序列相似性，收录了植物中的直系同源基因（orthologous genes）相关信息。该数据库旨在将自身作为一系列资源与数据库的“枢纽”，实现各类承载不同生物信息的数据库之间的双向关联。用户可通过氨基酸信息或关键词检索该数据库，在不同类群的生物中查找直系同源基因。
PGDBj“氨基酸序列数据库（amino acid sequence DB）”收录了来自20种归类于绿色植物亚界（Viridiplantae）的植物的50万条氨基酸序列。PGDBj直系同源基因数据库提供基于氨基酸序列相似性的基因簇（gene cluster）信息。研究人员对20个绿色植物亚界物种的50余万条氨基酸序列进行了双向BLAST（reciprocal BLAST）比对并完成聚类。来自植物基因组数据库（如TAIR10与RAP-DB）的序列也被纳入该聚类结果，并可直接链接至原始数据库。为在绿色植物亚界的比较分析中提供外类群（outgroups），研究团队同时对源自蓝细菌门（Cyanobacteria）与后口动物亚界（Deuterostomia）的直系同源数据集开展分析。