Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases
Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases
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DOI：
10.1093/pcp/pct189
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发表时间：
2014-01-01
影响因子：
4.9
通讯作者：
Tabata, Satoshi
中科院分区：
文献类型：
--
作者：
Asamizu, Erika;Ichihara, Hisako;Tabata, Satoshi
日本植物基因组数据库（PGDBj，http://pgdbj.jp/?ln=en）是一个门户网站，旨在整合数据库 (DB) 和文献中的植物基因组相关信息。 PGDBj 由三个组件数据库和一个交叉搜索引擎组成，该引擎提供对数据库内容的无缝搜索。三个DB如下。 (i) Ortholog DB，根据氨基酸序列相似性提供基因簇信息。对 20 个 Viridiplantae 物种的超过 500,000 个氨基酸序列进行了相互 BLAST 搜索并聚类。来自植物基因组数据库（例如 TAIR10 和 RAP-DB）的序列也包含在簇中，并与原始数据库直接链接。 (ii)植物资源数据库，整合了SABRE数据库，提供了RIKEN生物资源中心和国家生物资源项目积累和维护的cDNA和基因组序列资源。 (iii) DNA 标记数据库，提供来自文献和外部数据库的 DNA 标记、数量性状基因座和相关连锁图谱的手动或自动整理信息。由于 PGDBj 针对各种植物物种，包括模式植物、藻类以及作为食品、饲料和生物燃料的重要作物，因此鼓励基础生物学领域以及广泛农艺领域的研究人员使用感兴趣的 DNA 序列、基因名称、性状和表型进行搜索。 PGDBj 将从组件 DB 和各种类型的链接外部 DB 中返回搜索结果。
The Plant Genome DataBase Japan (PGDBj, http://pgdbj.jp/?ln=en) is a portal website that aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search over the contents of the DBs. The three DBs are as follows. (i) The Ortholog DB, providing gene cluster information based on the 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. (ii) The Plant Resource DB, integrating the SABRE DB, which provides cDNA and genome sequence resources accumulated and maintained in the RIKEN BioResource Center and National BioResource Projects. (iii) The DNA Marker DB, providing manually or automatically curated information of DNA markers, quantitative trait loci and related linkage maps, from the literature and external DBs. As the PGDBj targets various plant species, including model plants, algae, and crops important as food, fodder and biofuel, researchers in the field of basic biology as well as a wide range of agronomic fields are encouraged to perform searches using DNA sequences, gene names, traits and phenotypes of interest. The PGDBj will return the search results from the component DBs and various types of linked external DBs.