NAR Molecular Biology Database Collection entry number 505

http://imgt3d.igh.cnrs.fr/PrimerDB/Query_PrDB.pl

Folch G.^1,2, Bertrand J.¹, Lemaitre M.² and Lefranc M.-P.¹

¹, Université Montpellier II, CNRS, Montpellier, FRANCE
²EUROGENTEC S.A. Seraing, BELGIUM

Contact lefranc@ligm.igh.cnrs.fr

IMGT/PRIMER-DB is the IMGT oligonucleotide (primer) database for the immunoglobulins (IG) and T cell receptors (TR). The IG and TR primers are useful for combinatorial library constructions, scFv, phage display or microarray technologies. IMGT/PRIMER-DB is part of IMGT, the international ImMunoGeneTics information system®, http://imgt.cines.fr (1), 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/PRIMER-DB contains information on primers and combinations of primers described as "sets" [primers sharing identical properties (species, group and orientation)] and "couples" [sets of opposite orientation for which IMGT/LIGM-DB sequences are known (or expected)]. Primers, Sets and Couples are described in IMGT Primer cards, IMGT Set cards and IMGT Couple cards, respectively.An IMGT Primer is an oligonucleotide described by comparison to an IMGT/LIGM-DB reference sequence, according to the standardized rules of the IMGT Scientific chart, based on IMGT-ONTOLOGY (2). Taxonomy species and IMGT classification (group, subgroup, gene, allele) of a primer are those of the IMGT/LIGM-DB reference sequence, and not those of the PCR amplification products. This provides the following advantages for the data standardization: IMGT/PRIMER-DB primer definition, classification and description are independent from the experimental conditions, from DNA sources and from the different combinations (sets and couples) in which the primer can be used. That means that (i) the specificity of a primer (subgroup, gene or allele specific) which is either described experimentally or deduced from sequence comparison is not used for the primer classification, although these data are provided in the IMGT/PRIMER-DB Primer card in "Classification comments and specificity", (ii) the sequences resulting from the PCR amplifications are uniquely associated to the couples. The IMGT Primer cards are linked to IMGT/LIGM-DB flat files, IMGT Colliers de Perles and IMGT Repertoire Alignments of alleles of the IMGT/LIGM-DB reference sequence used for the primer description. IMGT/PRIMER-DB, developed by LIGM (http://imgt.cines.fr/textes/IMGTinformation/LIGM.html) in collaboration with UROGENTEC S.A. (Seraing, Belguim) (http://www.eurogentec.be/hp/hp.htm), has been on the Web since February 2002.

In July 2003, IMGT/PRIMER-DB contained 292 entries from Homo sapiens and Mus musculus

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. Lefranc, M.-P., IMGT, the international ImMunoGeneTics database®, Nucleic Acids Res., 2003, 31, 307-310, PMID:12520009
2. Giudicelli, V. and Lefranc, M.-P. Ontology for immunogenetics: the IMGT-ONTOLOGY, Bioinformatics, 1999, 15, 1047-1054, PMID: 10745995

Go to the abstract in the NAR 2003 Database Issue.

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