Go to the abstract in the NAR 2001 Database Issue.
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Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
Contact jrobinso@ebi.ac.uk
In 1998 the IMGT/HLA database was publicly released, this provided a centralised repository for the sequences of the alleles named by the WHO Nomenclature Committee for Factors of the HLA System. Since this time the database has grown and is the primary source of information for the study of sequences of the human major histocompatibilty complex. The HLA complex is located within the 6p21.3 region on the short arm of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and these include the 21 highly polymorphic HLA genes which influence the outcome of clinical transplantation and confer susceptibility to a wide range of non-infectious diseases. The initial release of the database contained a limited number of tools. These include allele reports, alignment tools, and detailed descriptions of the source cells. The online IMGT/HLA submission tool allows both new and confirmatory sequences to be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System. The latest releases demonstrate how the database has developed over the past two years. As a result of feedback from our users and developments in both bioinformatics and HLA we have been able to provide new tools and facilities. These have included the analysis of the ambiguous allele combinations as found in sequencing based typing (SBT). The latest tools include online searches of the ambiguous typing combinations and polymorphism identification tools. The tools initially released with the database have also been updated to better suit the user's needs, for example allele searches can now be performed on both the allele name and component EMBL/GenBank/DDBJ entry's accession number. The HLA sequences themselves have also been extended to include intron sequences and the 3¢ and 5¢ untranslated regions into the alignments and also the inclusion of new genes like MICA. On average an additional 75 new and confirmatory sequences are included in each quarterly releases of the database. The latest version (release 1.11.0 July 2001) contains 1437 HLA alleles derived from over 3600 component sequences from the EMBL/GenBank/DDBJ databases. As well as the ongoing development of the IMGT/HLA database, we are collaborating with other research groups to develop parallel databases for other species, which will include non-human primates, cows, chickens and dogs.
The IMGT/HLA database has been expanded to include intronic sequences for some of the loci. Analysis of the ambiguous allele combinations, as found in sequencing based typing (SBT), has recently been incorporated.
Peter Parham, Stanford University, USA. Peter Stoehr, European Bioinformatics Institute, UK.
Category Protein Databases
Go to the abstract in the NAR 2001 Database Issue.