Go to the abstract in the NAR 2003 Database Issue.
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http://www.ebi.ac.uk/imgt/mhc/
Robinson, J1, Waller, MJ1, de Groot, N2, Bontrop, R2, Kennedy, L3, Marsh, SGE1
1Anthony Nolan Research Institute, London, UK
2Biomedical Primate Research Centre, Rijswijk, The Netherlands
3Centre for Intergrated Genomic Medical Research, Manchester, UK
Contact jrobinso@ebi.ac.uk
The IMGT/HLA database has established a working system for the study of the sequences of the human MHC region. Using this system as a model, a more wide-ranging project has been implemented. The MHC sequences of many different species have been reported and different nomenclature systems used in the naming and identification of new genes and alleles. The IMGT/MHC project works as centralised platform for the publication of these sequences. If the sequences of different species can all be collated in a central resource using a unified approach, this can aid in the study of the MHC in all species. The first release of the IMGT/MHC database works with groups specialising in non-human primates, canines and felines. The initial species coverage includes 5 species of ape, 16 species of new world monkey, 17 species of old world monkey and 5 species of canines. The nomenclature of each species is the responsibility of the species nomenclature committees. These committees prepare the allele information in a standardised format which allows it to be quickly loaded into the database and then published via the website. The website content varies between species but all contain common features. The sequence alignments and nomenclature reports are made available for online searches. The nomenclature reports provide details of the alleles, previous designations, EMBL/GenBank/DDBJ accession numbers and references (where possible linked to PubMed). The alignments follow the same format as that used in the IMGT/HLA database, which can itself been seen as a subset of IMGT/MHC. Examples of other information found within each subset include allele distributions and taxonomic information. The IMGT/MHC system has a standardised interface for viewing the alignments and nomenclature tables. In all species the loci and files available are determined by the species. Once a species is selected the user can select the type of data and locus. The interface is also included on the top of the output, to allow the user to perform multiple queries without returning to the main species index. The initial release contains only a limited number of species and a small number of tools. As the database grows and more species are added, many of the tools already seen in the IMGT/HLA system will be incorporated into the website. The files will also be made available to download from the IMGT/MHC website, ftp server and included into SRS, BLAST and FASTA search engines. One facility that we hope to include is cross-species comparisons allowing further evolutionary studies of the MHC region.
Peter Stoehr, European Bioinformatics Institute, UK
Category Protein Databases
Go to the abstract in the NAR 2003 Database Issue.