PGDBj Ortholog Database

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.

日本植物基因组数据库（Plant Genome Database Japan，缩写PGDBj）旗下构建的PGDBj直系同源数据库，基于对应氨基酸序列的相似性，收录了植物中直系同源基因的相关信息。该数据库将自身定位为一系列资源与数据库的“枢纽”，旨在实现包含各类生物信息的数据库之间的双向互联。用户可通过氨基酸序列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”收录了来自绿色植物亚界（Viridiplantae）20个植物物种的50万条氨基酸序列。PGDBj直系同源数据库提供基于氨基酸序列相似性构建的基因簇信息，研究团队对20个绿色植物亚界物种的50余万条氨基酸序列开展了双向BLAST检索并完成聚类。来自植物基因组数据库（如TAIR10、RAP-DB）的序列也被纳入该基因簇，并附带指向原始数据库的直接链接。为在绿色植物亚界比较分析中设置外类群，研究团队同时还对源自蓝细菌门（Cyanobacteria）和后口动物亚界（Deuterostomia）的直系同源数据集开展了分析。

搜集汇总

背景与挑战

背景概述

PGDBj Ortholog Database 是由日本植物基因组数据库（PGDBj）创建的植物同源基因数据库，基于氨基酸序列相似性提供信息。它整合了20种绿色植物超过50万条序列的聚类结果，并链接至原始基因组数据库，同时包含用于比较分析的外群数据。