Database Description
| General information of database | ||||||||||
Database name
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PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods
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Alternative name
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PGDBj Marker, Map and Basic Information | |||||||||
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DOI
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10.18908/lsdba.nbdc01194-01-000.V003 |
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Version
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Creator
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Creator Name
Taeko Shibaya
Creator Affiliation
Kazusa DNA Research Institute
Literature Search
Creator Name
Hisako Ichihara 
Creator Affiliation
Osaka University
Literature Search
Creator Name
Sachiko Shirasawa
Creator Affiliation
Kazusa DNA Research Institute
Creator Name
Erika Asamizu
Creator Affiliation
Ryukoku University
Literature Search
Creator Name
Yasukazu Nakamura 
Creator Affiliation
Kazusa DNA Research Institute
Literature Search
Creator Name
Hideki Hirakawa
Creator Affiliation
Kazusa DNA Research Institute
Literature Search
Creator Name
Akihiro Nakaya
Creator Affiliation
Osaka University
Literature Search
Creator Name
Satoshi Tabata*
Creator Affiliation
Kazusa DNA Research Institute
Literature Search
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Contact address
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Kazusa DNA Research Institute 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 JAPAN 
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Database classification
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Plant Databases
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Database description
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DNA marker and gene map are used for useful gene identification with gene analysis, genome structure comparison and application researches such as marker selective breeding and DNA fingerprinting. We have selected 65 plants (mainly horticultural crop) and aggregated and marshalled their DNA markers (65 plants), QTLs related with important agronomic trait and gene maps (45 plants) from articles and other databases. We published the results in this database. We have also aggregated, marshalled and published basic information, gene analysis method and links to related web sites about 80 plants. |
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Features and manner of utilization of database
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Information of DNA markers and QTLs are curated manually from the published literature. The marker information includes marker sequences, genotyping methods, population and linkage map, and the results of population genetic analyses. The QTL information includes the genetic effects, chromosomal positions, and LOD scores. Website links are classified according to the content (e.g. Genome database and Expression database). User can search information about DNA marker, QTL, and website links by keywords such as marker name, agricultural trait, and classification of website links. |
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License
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CC BY-SA Detail | |||||||||
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Background and funding
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Name
Database Integration Coordination Program (FY2011-FY2013) "Integration of plant databases based on genome information" : National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (JST)
Name
Database Integration Coordination Program (FY2014-FY2016) "Plant Genome DataBase Japan (PGDBj) for integration of plant genome-related resources and information" : National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (JST)
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Reference(s)
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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
External Links
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.
External Links
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| Original website information | ||||||||||
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Database maintenance site
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URL of the original website
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http://pgdbj.jp/pages/index.html?dir=&page=mk&ln=en | |||||||||
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Operation start date
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8 August, 2012 | |||||||||
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Last update date
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31 March, 2017 | |||||||||
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URL of the portal site
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http://pgdbj.jp/?ln=en | |||||||||
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Whole data download
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- | |||||||||
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Referenced database
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- |
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Entry list
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Not available | |||||||||
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Query search
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Not available | |||||||||
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Web services
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Not available | |||||||||
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URL of Web services
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- | |||||||||
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Need for user registration
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Not available | |||||||||