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IMGT/LIGM-DB


NAR Molecular Biology Database Collection entry number 504
Duroux, P., Giudicelli, V., Jabado-Michaloud, J., Regnier, L., Lefranc, M.-P.
Université Montpellier 2, CNRS, Montpellier, France.

Database Description

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 (http://www.imgt.org/textes/IMGTinformation/LIGM.html), Montpellier, France, on the Web since July 1995 (1). IMGT/LIGM-DB is the first and the largest database of IMGT®, the international ImMunoGeneTics information system® (2,3), the high-quality integrated knowledge resource specialized in IG, TR, major histocompatibility complex (MHC) of human and other vertebrate species, and related proteins of the immune system (RPI) that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). 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 receives IG and TR sequences 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 (4,5) and on the IMGT-ONTOLOGY axioms and concepts (6,7), specific detailed annotations are added to IMGT flat files in a second step. The IMGT/LIGM-DB Web interface allows searches according to immunogenetic criteria and is easy to use without any knowledge of a computing language. All IMGT/LIGM-DB information is available through five modules of search: Catalogue, Taxonomy and characteristics, Keywords, Annotation labels, References. The current selection is displayed at the top of the resulting sequences pages, so users can check their 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 eight 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 and EMBL flat file. Selecting the "Subsequences" option allows users 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, Institut Pasteur). In April 2008, IMGT/LIGM-DB contained 122,425 sequences of IG and TR from human and 221 other vertebrate species.

Recent Developments

IMGT/Automat (8) is a tool which allows the automatic annotation of human and mouse cDNAs in IMGT/LIGM-DB using the results from IMGT/V-QUEST (9) and IMGT/JunctionAnalysis (10).

Acknowledgements

IMGT® received funding from the European Union (EU) programmes BIOMED1 (BIOCT930038), BIOTECH2 (BIO4CT960037), 5th PCRDT (QLG2-2000-01287) and 6th PCRDT (ImmunoGrid IST-028069), from the Agence Nationale de la Recherche ANR (BIOSYS06-135457) and from the Région Languedoc-Roussillon. IMGT® is funded by the Centre National de la Recherche Scientifique (CNRS), the Ministère de l'Education Nationale and the Ministère de la Recherche.

References

1. Giudicelli V., Ginestoux C., Folch G., Jabado-Michaloud J., Chaume D. and Lefranc, M.-P. IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences, Nucleic Acids Res., 2006, 34, D781-D784, PMID:16381979
2. Lefranc, M.-P., Giudicelli, V., Kaas, Q., Duprat, E., Jabado-Michaloud, J., Scaviner, D., Ginestoux, C., Clément, O., Chaume, D., and Lefranc, G. (2005) IMGT, the international ImMunoGeneTics information system®. Nucleic Acids Res., 33, D593-D597.
3. Lefranc, M.-P., Clément, O., Kaas, Q., Duprat, E., Chastellan, P., Coelho, I., Combres, K., Ginestoux, C., Giudicelli, V., Chaume, D., and Lefranc, G. (2005) IMGT-Choreography for Immunogenetics and Immunoinformatics. In Silico Biology, 5, 45-60.
4. Lefranc, M.-P., and Lefranc, G. (2001) The Immunoglobulin FactsBook (http://www.imgt.org/textes/IMGTindex/factsbook.html), Academic Press, 458 pages, ISBN:012441351X
5. Lefranc, M.-P., and Lefranc, G. (2001) The T cell receptor FactsBook (http://www.imgt.org/textes/IMGTindex/factsbook.html), Academic Press, 398 pages, ISBN: 0124413528
6. Giudicelli, V., and Lefranc, M.-P. (1999) Ontology for immunogenetics: the IMGT-ONTOLOGY. Bioinformatics, 15, 1047-1054
7. Duroux, P., Kaas, Q., Brochet, X., Lane, J., Ginestoux, C., Lefranc, M.-P., and Giudicelli, V. (2008) IMGT-Kaleidoscope, the formal IMGT-ONTOLOGY paradigm. Biochimie, 90, 570-583.
8. Giudicelli, V., Chaume, D., Jabado-Michaloud, J., and Lefranc, M.-P. (2005) Immunogenetics sequence annotation: the strategy of IMGT based on IMGT-ONTOLOGY. Stud. Health Technol. Inform., 116, 3-8.
9. Giudicelli, V., Chaume, D., and Lefranc, M.-P. (2004) IMGT/V-QUEST, an integrated software for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Res., 32, W435-W440.
10. Yousfi Monod, M., Giudicelli, V., Chaume, D., and Lefranc, M.-P. (2004) IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics, 20, i379-i385.


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