General information of database
info Alternative name Plant Genome Database Japan - Ortholog Database
info Creator
Creator Name:
Akihiro Nakaya*
Link to J-GLOBAL
Link to researchmap
Creator Affiliation:
Osaka University
Creator Name:
Hisako Ichihara
Creator Affiliation:
Kazusa DNA Research Institute
Creator Name:
Erika Asamizu
Link to J-GLOBAL
Link to researchmap
Creator Affiliation:
Ryukoku University
Creator Name:
Hideki Hirakawa
Link to J-GLOBAL
Link to researchmap
Creator Affiliation:
Kazusa DNA Research Institute
Creator Name:
Yasukazu Nakamura
Link to J-GLOBAL
Link to researchmap
Creator Affiliation:
Kazusa DNA Research Institute
Creator Name:
Satoshi Tabata
Creator Affiliation:
Kazusa DNA Research Institute
info Contact address Department of Genome Informatics, Graduate School of Medicine, Osaka University
2-2 Yamadaoka, Suita, Osaka 565-0871, JAPAN
E-mail: pgdbj_ortholog_db_address / pgdbj_ortholog_db_address2
info Database classification Protein sequence databases - Protein domain databases; protein classification
info Organism
Taxonomy Name:
Viridiplantae
Taxonomy Name:
Cyanobacteria
info Database description Orthology is a homologous relationship among genes derived from a common ancestor by speciation. Genes in such a relationship are referred to as orthologs or orthologous genes and provide important clues to clarify the process of genome evolution and to predict the divergence of gene function based on syntenic relationships among species. PGDBj Ortholog DB is a database that provides orthologous relationships of genes that are computationally determined according to similarities between amino acid sequences, and currently consists of 40 species of Viridiplantae (green plants) and 213 species of Cyanobacteria (blue-green algae).
info Features and manner of utilization of database PGDBj Ortholog DB is hierarchically organized to reflect evolutionary relationships among species and taxa. By connecting entries of multiple plant genome databases to this database, PGDBj Ortholog DB can work as a hub database and provide a way to gather and organize the relevant data in the databases. By submitting queries to the PGDBj Ortholog DB with keywords or amino acid sequences, users can obtain the list of the links to the relevant entries of the plant genome databases in relation to the functions and characteristics of genes across various species and taxa including both model plants and crop plants. Following the links obtained, users can retrieve the actual entries from the databases.
info Background and funding
info Reference(s)
Article title:
Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases
Author name(s):
Erika Asamizu, Hisako Ichihara, Akihiro Nakaya, Yasukazu Nakamura, Hideki Hirakawa, Takahiro Ishii, Takuro Tamura, Kaoru Fukami-Kobayashi, Yukari Nakajima and Satoshi Tabata
Journal:
Plant Cell Physiol (2014) 55 (1): e8.
Article title:
Plant Genome DataBase Japan (PGDBj).
Author name(s):
Akihiro Nakaya, Hisako Ichihara, Erika Asamizu, Shirasawa Sachiko, Yasukazu Nakamura, Satoshi Tabata and Hideki Hirakawa
Journal:
Methods Mol Biol (2017) 1533: 45-77.
Original website information
info Database maintenance site Kazusa DNA Research Institute
info Operation start date August, 2012
info Last update date December, 2016
info Referenced database
- NCBI RefSeq, NCBI Taxonomy
- Eucalyptus camaldulensis Genome Database
- Jatropha Genome Database
- Lotus japonicus Genome Sequencing Project
- Tomato SBM Database
- Trifolium pratense EST Index
- Chlamydomonas reinhardtii EST Index
- Lotus japonicus EST Index
- Arabidopsis thaliana EST Index
- Porphyra yezoensis EST Index
- MiBASE Micro-Tom Database
- The Rice Annotation Project Database (RAP-DB)
- Rice TOGO Browser
- The Rice Expression Profile Database (RiceXPro)
- SALAD Database
- The Arabidopsis Information Resource (TAIR)
- RIKEN Arabidopsis Genome Encyclopedia (RARGE)
- RIKEN Populus Database (RPOPDB)
- Triticeae Full-Length CDS Database (TriFLDB)
- KEGG/GENES
- PHYSCObase
info Entry list Available
info Query search Available
info Web services Not available
info URL of Web services -
info Need for user registration Not available