databases
Introduction
A range of databases exist which manage information relating to
Brassica genetics, genomics and related activities. A number of these are under active development, and more are expected to arise in coming years. A major challenge is the need for standardisation of nomenclature and establishment of management of 'registries' of widely used resources and information.
Links to external databases
BrassicaDB
BrassicaDB 
was funded until 2003 by BBSRC under the UK-CropNet programme. It aimed to curate a comprehensive set of sequence accessions, bibliography, and a range of genetic maps, markers etc. In addition, this database is currently the original source of information for the 'BBSRC set' of Brassica SSR markers. Martin Trick at JIC ensures that the database is still automatically refreshed with newly deposited Brassica sequences every night and is occasionally rebuilt from scratch. There is also a useful
Brassica BLAST server associated with this database.
CropStoreDB - NEW SITE
CropStoreDB is a relational database that provides a framework for standardised curation and management of data relating to crop genetics. We have adopted
Brassica as an exemplar use-base. The CropStore data curation pipeline and database system is being used to collate reference information for the MBGP data repository, including interfaces developed direct through this website, and available using the links below:
Ensembl (Arabidopsis)
The Ensembl genome browser implementation at
NASC (
AtEnsembl ) provides access to definitive annotation of the Arabidopsis genome (TAIR7), with additional tracks that indicate alignment of homologous
Brassica sequences, such s ESTs, BACs etc.
Physical maps
Several projects have generated fingerprint and hybridisation data relating to long cloned sequences of
Brassica, mostly in BAC libraries. Databases that manage these data include:
MBrGSP BAC registry
This database holds
information about the status of BACs being sequenced within the
Brassica rapa Genome Sequencing Project, with the data published via this website. Contact:
Jun Wang
A new implementation of BrassEnsembl has been developed at Rothamsted Research in order to provide a
Brassica-centric view of the emerging 'A' genome sequence data. This will use a 'pseudochromosome' coordinate system to which will be assigned seqeuenced BACs and sequence scaffolds, linking through to the BAC-by-BAC annotation at
JIC. To assist in the navigation between genetic and genomic data, there will also be links to consensus integrated genetic maps of the Brassica A and C genomes, placed in the context of collinearity blocks conserved with Arabidopsis.
SeqStore for Brassica
The SeqStore for
Brassica database has been developed at Rothamsted Research for the MBGP, and aims to provide a comprehesnive set of public domain sequence data derived from
Brassica species. This includes not only the latest GenBank records, but also sequence sets that have yet to be entered into the standard DNA repositories, but nevertheless are valuable resources as sequence-tagged markers. The concept of 'sequence_collections' has been established in order to provide useful subsets of sequences associated with particular clone libraries, genetic marker collections, etc. In addition, SeqStore for Brassica will be used to manage information relating to the agreed
gene nomenclature system. More detailed information will be about SeqStore will be published here during early 2009.
This Page Was Last Edited: 01-Jul-2010
