IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations

BACKGROUND: Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cell receptor (TR) loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS). Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files) and are difficult to extract. DESCRIPTION: IMGT/GeneInfo is an online information system that provides, through a user-friendly interface, exhaustive information resulting from the complex mechanisms of T cell receptor V-J and V-D-J recombinations. T cells comprise two populations which express the αβ and γδ TR, respectively. The first version of the system dealt with the Homo sapiens and Mus musculus TRA and TRB loci whose gene rearrangements allow the synthesis of the αβ TR chains. In this paper, we present the second version of IMGT/GeneInfo where we complete the database for the Homo sapiens and Mus musculus TRG and TRD loci along with the introduction of a quality control procedure for existing and new data. We also include new functionalities to the four loci analysis, giving, to date, a very informative tool which allows to work on V(D)J genes of all TR loci in both human and mouse species. IMGT/GeneInfo provides more than 59,000 rearrangement combinations with a full gene description which is freely available at . CONCLUSION: IMGT/GeneInfo allows all TR information sequences to be in the same spot, and are now available within two computer-mouse clicks. This is useful for biologists and bioinformaticians for the study of T lymphocyte V(D)J gene rearrangements and their applications in immune response analysis

IMGT/Automat: the strategy for the annotation of human and mouse cDNA nucleotide sequences of IG and TR

The cDNA sequences of immunoglobulins (IG) and T cell receptors (TR) represent more than one half of the sequences in the IMGT^®^ nucleotide database IMGT/LIGM-DB^1^ and 75% of them are from human and mouse. A few cDNA are germline but the great majority results from a V-D-J or V-J gene rearrangement, spliced to a C gene. The IG and TR genes have been studied extensively in IMGT^®^ ("http://www.imgt.org":http://www.imgt.org) ^2^, which allowed to set up their nomenclature and the corresponding germline reference sequences. These standardized reference directory sets (one for each group of each locus) and the IMGT-ONTOLOGY axioms and derived concepts^3^ are the key elements indispensable to perform the annotation of IG and TR cDNA sequences. A Java program, IMGT/Automat^4^, was developed by IMGT^®^, to automatically annotate the IG and TR cDNA sequences and to produce a totally automatic and complete annotation. More than 9,000 human and mouse cDNA have already been successfully automatically annotated. The quality of the cDNA automatic annotation is equivalent to the quality of the annotation achieved by a human expert. The IMGT^®^ strategy is currently the only way, in the field of immunogenetics, to guarantee the annotation quality and the management of an always increasing number of IG and TR cDNA nucleotide sequences