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Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases

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 cont...

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Autores principales: Asamizu, Erika, Ichihara, Hisako, Nakaya, Akihiro, Nakamura, Yasukazu, Hirakawa, Hideki, Ishii, Takahiro, Tamura, Takuro, Fukami-Kobayashi, Kaoru, Nakajima, Yukari, Tabata, Satoshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894704/
https://www.ncbi.nlm.nih.gov/pubmed/24363285
http://dx.doi.org/10.1093/pcp/pct189
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author Asamizu, Erika
Ichihara, Hisako
Nakaya, Akihiro
Nakamura, Yasukazu
Hirakawa, Hideki
Ishii, Takahiro
Tamura, Takuro
Fukami-Kobayashi, Kaoru
Nakajima, Yukari
Tabata, Satoshi
author_facet Asamizu, Erika
Ichihara, Hisako
Nakaya, Akihiro
Nakamura, Yasukazu
Hirakawa, Hideki
Ishii, Takahiro
Tamura, Takuro
Fukami-Kobayashi, Kaoru
Nakajima, Yukari
Tabata, Satoshi
author_sort Asamizu, Erika
collection PubMed
description 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.
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spelling pubmed-38947042014-01-17 Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases Asamizu, Erika Ichihara, Hisako Nakaya, Akihiro Nakamura, Yasukazu Hirakawa, Hideki Ishii, Takahiro Tamura, Takuro Fukami-Kobayashi, Kaoru Nakajima, Yukari Tabata, Satoshi Plant Cell Physiol Special Online Collection – Database Papers 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. Oxford University Press 2014-01 2014-01-10 /pmc/articles/PMC3894704/ /pubmed/24363285 http://dx.doi.org/10.1093/pcp/pct189 Text en © The Author 2013. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Special Online Collection – Database Papers
Asamizu, Erika
Ichihara, Hisako
Nakaya, Akihiro
Nakamura, Yasukazu
Hirakawa, Hideki
Ishii, Takahiro
Tamura, Takuro
Fukami-Kobayashi, Kaoru
Nakajima, Yukari
Tabata, Satoshi
Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases
title Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases
title_full Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases
title_fullStr Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases
title_full_unstemmed Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases
title_short Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases
title_sort plant genome database japan (pgdbj): a portal website for the integration of plant genome-related databases
topic Special Online Collection – Database Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894704/
https://www.ncbi.nlm.nih.gov/pubmed/24363285
http://dx.doi.org/10.1093/pcp/pct189
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