Databases


A range of databases exist which manage information relating to Brassica genetics, genomics and related activities. There remains achallenge to extend the scope of nomenclature standards, management of 'registries' of widely used resources and information, and development of tools for integrating and navigating between disparate datasets.

Genome browsers and associated sites


Links to external databases


BrassicaDB

BrassicaDB link 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 link associated with this database.

CropStoreDB

CropStore CropStoreDB link 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: CropStoreDB is a component of

InterStoreDB

is a suite of closely linked web-based tools, including CropStoreDB designed to assist researchers in navigating from phenotype to genotype. The initial implementation for InterStoreDB is for Brassica.

Ensembl (Arabidopsis)

The Ensembl genome browser implementation at NASC (AtEnsembl link) 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 that were being sequenced within the original Brassica rapa Genome Sequencing Project, with the data published via this website.







This Page Was Last Edited: 02-Jun-2016