BrassicaDB is a database of genetic and molecular information relating to Brassica species. At this time it concentrates only on Brassica napus, Brassica oleracea and Brassica rapa. The current data consists of two sets of genetic maps for the B. napus genome (each derived from a separate mapping population), a set of genetic maps from B. oleracea, the published nucleotide sequences from B. napus, B. oleracea and B. rapa and a bibliography. Further details of the current contents of the database can be found on the BrassicaDB website (http://jic-bioinfo.bbsrc.ac.uk/BrassicaDB/).
BrassicaDB is available in two forms:
Both forms are available locally within JIC from BrassicaDB at JIC (http://brassica.jic.bbsrc.ac.uk/). If you are outside the JIC then you will only be able to access the public version of the database.
All the examples in this tutorial are taken from the public version of the database.
The data is assembled in to groups called classes. In this section a brief overview of the classes in the databases is given and an indication of which classes are related.
Details of the AFLP (primers, etc.) used to detect the alleles and a list of detected alleles.
Description of the allele at a locus. Currently these just link the locus to the AFLP, microsatellite or probe used to detect the allele. When phenotypic traits are added the phenotype descriptions will be linked through here.
An authors list of publications.
A description of the product of a gene and the other sequences encoding the same product. This is based on the sequence annotation.
List of papers which occur in a journal.
The locus of an allele.
The genetic maps. The N maps are from B. napus and the O maps are from B. oleracea. The second part of the map name is the mapping population from which the map was derived.
Description of the mapping populations used to generate the genetic maps.
Description of the microsatellite used to detect an allele (primers, etc.) and a list of the detected alleles.
A comparison of two genetic maps.
Protein BLAST hits from SPTrEMBL.
Nucleotide BLAST hits from EMBL.
Bibliography entries for papers and sequences.
Description of the probe used to identify a locus (connected through allele).
The proteins encoded by the nucleotide sequences and those found by searching SPTrEMBL for B. napus, B. oleracea and B. rapa protein.
Nucleotide sequences for B. napus, B. oleracea and B. rapa obtained from EMBL.
This class is also available as two subclasses:
The EST sequences.
Genomic DNA sequences and other sequences which do not fall in the EST class.
Descriptions of the data sources from which data was obtained.
The public version of the database is also available at various mirror sites:
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Last modified: Mon Dec 4 14:21:29 GMT 2000 |
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