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BRAD V3.0: an upgraded Brassicaceae database

The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015...

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Autores principales: Chen, Haixu, Wang, Tianpeng, He, Xiaoning, Cai, Xu, Lin, Runmao, Liang, Jianli, Wu, Jian, King, Graham, Wang, Xiaowu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728314/
https://www.ncbi.nlm.nih.gov/pubmed/34755871
http://dx.doi.org/10.1093/nar/gkab1057
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author Chen, Haixu
Wang, Tianpeng
He, Xiaoning
Cai, Xu
Lin, Runmao
Liang, Jianli
Wu, Jian
King, Graham
Wang, Xiaowu
author_facet Chen, Haixu
Wang, Tianpeng
He, Xiaoning
Cai, Xu
Lin, Runmao
Liang, Jianli
Wu, Jian
King, Graham
Wang, Xiaowu
author_sort Chen, Haixu
collection PubMed
description The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the ‘Syntenic Gene @ Subgenome’ module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include ‘MicroSynteny’ for viewing synteny of selected fragment pairs, and ‘Polymorph’ for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.
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spelling pubmed-87283142022-01-05 BRAD V3.0: an upgraded Brassicaceae database Chen, Haixu Wang, Tianpeng He, Xiaoning Cai, Xu Lin, Runmao Liang, Jianli Wu, Jian King, Graham Wang, Xiaowu Nucleic Acids Res Database Issue The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the ‘Syntenic Gene @ Subgenome’ module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include ‘MicroSynteny’ for viewing synteny of selected fragment pairs, and ‘Polymorph’ for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community. Oxford University Press 2021-11-10 /pmc/articles/PMC8728314/ /pubmed/34755871 http://dx.doi.org/10.1093/nar/gkab1057 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Chen, Haixu
Wang, Tianpeng
He, Xiaoning
Cai, Xu
Lin, Runmao
Liang, Jianli
Wu, Jian
King, Graham
Wang, Xiaowu
BRAD V3.0: an upgraded Brassicaceae database
title BRAD V3.0: an upgraded Brassicaceae database
title_full BRAD V3.0: an upgraded Brassicaceae database
title_fullStr BRAD V3.0: an upgraded Brassicaceae database
title_full_unstemmed BRAD V3.0: an upgraded Brassicaceae database
title_short BRAD V3.0: an upgraded Brassicaceae database
title_sort brad v3.0: an upgraded brassicaceae database
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728314/
https://www.ncbi.nlm.nih.gov/pubmed/34755871
http://dx.doi.org/10.1093/nar/gkab1057
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