Plant Genome DataBase Japan (PGDBj).
Methods Mol Biol
; 1533: 45-77, 2017.
Article
em En
| MEDLINE
| ID: mdl-27987164
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.
Palavras-chave
Buscar no Google
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Plantas
/
Genoma de Planta
/
Biologia Computacional
/
Genômica
/
Bases de Dados de Ácidos Nucleicos
Tipo de estudo:
Prognostic_studies
País/Região como assunto:
Asia
Idioma:
En
Revista:
Methods Mol Biol
Ano de publicação:
2017
Tipo de documento:
Article