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

Links to external databases

  • AAFC Comparative Genome Viewer link
  • ATIDB with Brassica features link
  • BrassicaDB link
  • IMSORB genetic marker and qtl database link
  • Korea B. rapa genomics link
  • NASC Arabidopsis Ensembl with Brassica tracks link
  • TIGR B. oleracea GSS link
  • UK BBSRC Physical Mapping DB link

    • 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.

    CropStore

    CropStore is a relational database that provides a framework for standardised curation and management of data relating to crop genetics. The most comprehensive use-case is Brassica, and the system is being used to collate reference information for the MBGP data repository. more....

    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:
  • Brassica IGF project link (UK) fingerprint and hybridisation of B. rapa and B. oleracea libraries
  • Korean Sequencing project B. rapa BAC fingerprinting database link

    • SeqStore for Brassica

    The SeqStore for Brassica database is maintained 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 lates GenBank records, but also sequence sets that have yet to be entered into DNA repositories, but nevertheless are valuable resources as sequence-tagged markers. more....