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Published (Version of record)CC BY V4.0, Open Access
Published (Version of record)CC BY V4.0, Open
Journal article
BRAD V3.0: an upgraded Brassicaceae database
Nucleic Acids Research, Vol.50(D1), pp.D1432-D1441
07/01/2022
PMCID: PMC8728314
PMID: 34755871
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Abstract
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.
Details
- Title
- BRAD V3.0: an upgraded Brassicaceae database
- Creators
- Haixu Chen - Chinese Academy of Agricultural SciencesTianpeng Wang - Chinese Academy of Agricultural SciencesXiaoning He - Chinese Academy of Agricultural SciencesXu Cai - Chinese Academy of Agricultural SciencesRunmao Lin - Chinese Academy of Agricultural SciencesJianli Liang - Chinese Academy of Agricultural SciencesJian Wu - Chinese Academy of Agricultural SciencesGraham King - Southern Cross UniversityXiaowu Wang - Chinese Academy of Agricultural Sciences
- Publication Details
- Nucleic Acids Research, Vol.50(D1), pp.D1432-D1441
- Publisher
- Oxford University Press
- Grant note
- National Programon Key Research Project [2021YFF1000047]; National Natural Science Foundation of China [31630068]; National Program on Key Research Project [2016YFD0100307]; Agricultural Science and Technology Innovation Program (ASTIP); Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, P.R. China. Funding for open access charge: Research projects funded to Xiaowu Wang.
- Identifiers
- 991012982359502368
- Copyright
- © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. 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.
- Academic Unit
- Faculty of Science and Engineering; School of Environment, Science and Engineering; Science; Southern Cross Plant Science
- Language
- English
- Resource Type
- Journal article