BrassicaDB is a database of genetic and molecular information derived from key Brassica species.
It comprises exclusively Brassica napus (oilseed rape), Brassica oleracea (cabbage) and Brassica rapa (turnip).
BrassicaDB contains data in the following areas:
Three sets of genetic maps are available for Brassica napus (one based on publicly available Microsatellite markers, integrated with a framework of RFLP markers whose sequences are now also in the public domain), four sets for Brassica oleracea and one set for Brassica rapa. Each set of maps is derived from a different mapping population but largely uses a common set of RFLP probes and, often, common parents.
The loci on the genetic maps.
Most of the loci in the database have been identified using RFLP probes. For each probe there is an entry in the database identifying the corresponding loci.
Published DNA sequences from Brassica napus, Brassica oleracea and Brassica rapa have been included in the database. As these sequences are mapped they will be added to the maps. Links to the nucleotide sequence databases are provided.
A list of protein sequences from Brassica napus, Brassica oleracea and Brassica rapa is included in the database, and links to protein databases are provided.
A large bibliography has been created and added to BrassicaDB. This is currently focused on Brassica napus and Brassica oleracea, but will be expanded to include other Brassica species, as they are included in the database.
Where further information is available from a public resource on the Internet, links are included to allow for further data investigation.
The Java applet below will attempt to make a connection to a copy of the Public version of BrassicaDB and get the current set of details from the database. If your browser is unable to run the applet, then a static set of details will be displayed.
Instead a static listing (23/07/2002) follows:
Cross-links to other on-line data sources are seen as an important way of minimizing the size of the database, and keeping information up to date. At the moment BrassicaDB supports cross-links for the following data:
The Brassica napus genome has a high level of internal duplication. This means that there are homologies within the genome. It is hoped that BrassicaDB will document these homologies and provide tools for visualization of these homologies (GridMap). As the number of brassica species in the database increases, each new genome will be integrated into this scheme, allowing easy visulisation of cross genome homologies as well.
It is also hoped that homologies with Arabidopsis, will also be documented and that the same visualization tools will provide a convenient way to view them. This part of the project is being developed within the UK CropNet with the intention of linking all the species databases together through homology data. For more information see the UK CropNet web site.
The following data is to be added to the database:
You can contact us if you have any problems or queries about BrassicaDB.
Martin Trick (PI-developer/curator)John Innes Centre