NAR Molecular Biology Database Collection entry number 504

http://imgt.cines.fr/cgi-bin/IMGTlect.jv

Chaume, D., Giudicelli, V., Lefranc, M.-P.

Université Montpellier II, CNRS, Montpellier, FRANCE

Contact lefranc@ligm.igh.cnrs.fr

IMGT/LIGM-DB is the IMGT comprehensive database of immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences, from human and other vertebrate species, with translation for fully annotated sequences, created in 1989 by LIGM, Montpellier, France, on the Web since July 1995 (1-3). IMGT/LIGM-DB is the first and the largest database of IMGT, the international ImMunoGeneTics information system® (3), the high-quality integrated knowledge resource specializing in IG, TR, major histocompatibility complex (MHC), and related proteins of the immune system (RPI) of human and other vertebrate species. IMGT/LIGM-DB sequence data are identified by the EMBL/GenBank/DDBJ accession number. The unique source of data for IMGT/LIGM-DB is EMBL which shares data with GenBank and DDBJ. Once the sequences are allowed by the authors to be made public, LIGM automatically receives IG and TR sequences by e-mail from the European Bioinformatics Institute EBI. After control by LIGM curators, data are scanned to store sequences, bibliographical references and taxonomic data, and standardized IMGT/LIGM-DB keywords are assigned to all entries. Based on expert analysis (4-7), specific detailed annotations are added to IMGT flat files in a second step. The IMGT/LIGM-DB Web interface allows searches according to immunogenetic specific criteria and is easy to use without any knowledge in a computing language. All IMGT/LIGM-DB information is available through five modules of search: Catalogue, Taxonomy and characteristics, Keywords, Annotation labels, References. Selection is displayed at the top of the resulting sequences pages, so the user can check one's own queries. It is possible to modify the request or to consult the results. Selecting the "View" option provides a list of resulting sequences. Selection of one sequence in the list offers nine possibilities: annotations, IMGT flat file, coding regions with protein translation, catalogue and external references, sequence in dump format, sequence in FASTA format, sequence with three reading frames, EMBL flat file, and IMGT/V-QUEST. Selecting the "Subsequences" option allows to search for sequence fragments (subsequences) corresponding to a particular label for the resulting sequences (available for fully annotated sequences). IMGT/LIGM-DB data are also distributed by anonymous FTP servers at CINES (ftp://ftp.cines.fr/IMGT/) and at EBI (ftp://ftp.ebi.ac.uk/pub/databases/imgt/), and from many SRS (Sequence Retrieval System) sites. IMGT/LIGM-DB can be searched by BLAST or FASTA on different servers (e.g., EBI, IGH, INFOBIOGEN, Institut Pasteur). In July 2003, IMGT/LIGM-DB contained 74,474 sequences of IG and TR from human and 104 other vertebrate species.

IMGT/Automat (8) is a new tool which allows automatic annotations of human and mouse cDNAs in IMGT/LIGM-DB.

IMGT is funded by the European Union's 5th PCRDT programme QLG2-2000-01287, the Centre National de la Recherche Scientifique (CNRS), the Ministère de l'Education Nationale and the Ministère de la Recherche.

1. Giudicelli, V., Chaume, D., Bodmer, J., Müller, W., Busin, C., Marsh, S., Bontrop, R., Lemaitre, M., Malik, A., and Lefranc, M.-P. IMGT, the international ImMunoGeneTics database, Nucl. Acids Res., 1997, 25, 206-211 PMID:9016537
2. Lefranc M.-P. IMGT, the international ImMunoGeneTics database®: a high-quality information system for comparative immunogenetics and immunology, Dev. Comp. Immunol., 2002, 26, 697-705, PMID:12206833
3. Lefranc, M.-P., IMGT, the international ImMunoGeneTics database®, Nucleic Acids Res., 2003, 31, 307-310, PMID:12520009
4. Lefranc M.-P. and Lefranc G., The Immunoglobulin FactsBook, Academic Press, Harcourt, 458 pages, 2001, ISBN:012441351X
5. Lefranc M.-P. and Lefranc G., The T cell receptor FactsBook, Academic Press, Harcourt, 398 pages, 2001, ISBN:0124413528
6. Giudicelli, V. and Lefranc, M.-P. Ontology for immunogenetics: the IMGT-ONTOLOGY, Bioinformatics, 1999, 15, 1047-1054, PMID: 10745995
7. Lefranc, M.-P., Pommié, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L., Thouvenin-Contet, V. and Lefranc, G. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains, Dev. Comp. Immunol., 2003, 27, 55-77, PMID:12477501
8. Giudicelli, V., The IMGT strategy for the automatic annotation of IG and TR cDNA sequences: IMGT/Automat, European Conference on Computational Biology, ECCB 2003

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