title: Plant Genome DataBase Japan (PGDBj): a portal website for the integration of plant genome-related databases.
abstract: 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.
authors.affiliation: Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba, 292-0818 Japan.
authors.forename: Erika
authors.initials: E
authors.lastname: Asamizu
authors.forename: Hisako
authors.initials: H
authors.lastname: Ichihara
authors.forename: Akihiro
authors.initials: A
authors.lastname: Nakaya
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Hideki
authors.initials: H
authors.lastname: Hirakawa
authors.forename: Takahiro
authors.initials: T
authors.lastname: Ishii
authors.forename: Takuro
authors.initials: T
authors.lastname: Tamura
authors.forename: Kaoru
authors.initials: K
authors.lastname: Fukami-Kobayashi
authors.forename: Yukari
authors.initials: Y
authors.lastname: Nakajima
authors.forename: Satoshi
authors.initials: S
authors.lastname: Tabata
mesh_terms: D002874:Chromosome Mapping; D030541:Databases, Genetic; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics*; D020407:Internet; D007564:Japan; D040641:Quantitative Trait Loci / Q000235:genetics; D017386:Sequence Homology, Amino Acid
chemical_list: D005819:Genetic Markers
keywords: DNA marker; Database integration; Ortholog; Plant genome; Plant resource; QTL