title: Plant Genome DataBase Japan (PGDBj).
abstract: A portal website that integrates a variety of information related to genomes of model and crop plants from databases (DBs) and the literature was generated. This website, named the Plant Genome DataBase Japan (PGDBj, http://pgdbj. jp/en/ ), is comprised of three component DBs and a cross-search engine which provides a seamless search over their contents. One of the three component DBs is the Ortholog DB, which provides gene cluster information based on the amino acid sequence similarity. Over 1,000,000 amino acid sequences of 40 Viridiplantae species were collected from the public DNA DBs, and plant genome DBs such as TAIR and RAP-DB were subjected to reciprocal BLAST searches for clustering. Another component DB is the Plant Resource DB for genomic- and bio-resources. This DB also integrates the SABRE DB, which provides cDNA and genome sequence resources maintained in the RIKEN BioResource Center and National BioResource Projects Japan. The third component DB of PGDBj is the DNA Marker DB, which manually or automatically collects curated information on DNA markers, quantitative trait loci (QTL), and related genetic linkage maps, from the literature and external DBs. By combining these component DBs and a cross-search engine, PGDBj serves as a useful platform to study genetic systems for both fundamental and applied researches for a wide range of plant species.
authors.affiliation: Department of Genome Informatics, Graduate School of Medicine, Osaka University, 1-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Nakaya
authors.affiliation: Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan.
authors.forename: Hisako
authors.initials: H
authors.lastname: Ichihara
authors.affiliation: Department of Plant Life Sciences, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan.
authors.forename: Erika
authors.initials: E
authors.lastname: Asamizu
authors.affiliation: Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan.
authors.forename: Sachiko
authors.initials: S
authors.lastname: Shirasawa
authors.affiliation: Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan.
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakamura
authors.affiliation: Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
authors.affiliation: Department of Technology Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan. hh@kazusa.or.jp.
authors.forename: Hideki
authors.initials: H
authors.lastname: Hirakawa
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D007564:Japan; D010944:Plants / Q000235:genetics* / Q000378:metabolism; D040641:Quantitative Trait Loci; D057386:Search Engine; D014584:User-Computer Interface; D064878:Web Browser
chemical_list: D005819:Genetic Markers
keywords: DNA marker; Ortholog; PGDBj; Plant bioresource; Plant genomics