The IMGT Strategy For The Automatic Annotation of IG And TR cDNA Sequences: IMGT/Automat

IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr) [1] created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM), at the Université Montpellier II, CNRS, Montpellier, France, is a high quality integrated information system, specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrates. IMGT/LIGM-DB, the first and the largest IMGT sequence database, includes 69,616 nucleotidic sequences of 105 species in May 2003. We developed IMGT/Automat, an integrated IMGT Java tool, to automatically perform the annotation of the rearranged cDNA sequences which represent the half of the IMGT/LIGM-DB content. The annotation procedure includes the IDENTIFICATION of the sequences, the CLASSIFICATION of the IG and TR genes and alleles, and the DESCRIPTION of all IG and TR specific and constitutive motifs within the nucleotidic sequences, according to the IDENTIFICATION (standardized keywords), CLASSIFICATION (gene nomenclature), DESCRIPTION (standardized labels) and NUMEROTATION (IMGT unique numbering) concepts of IMGT/ONTOLOGY [2]. IMGT/Automat performs these tasks with the help of two available IMGT on-line tools: IMGT/V-QUEST (http://imgt.cines.fr) for the gene and allele identification and delimitations, and IMGT/JunctionAnalysis (http://imgt.cines.fr) for a detailed analysis of the junction in rearranged sequences. Because IMGT focuses on the quality of expertly annotated IG and TR sequences, we were aware that a such annotation tool must be as reliable and accurate as a human annotator is. Accuracy and reliability of the annotation are mainly estimated by the programme it-self with the evaluation of: the IMGT/V-QUEST alignment scores, the deduced sequence functionality, and the coherence of the characterized and delimited IG and TR motifs. IMGT/Automat is currently used by the IMGT team. It has performed the annotation of 7418 cDNA IG and TR sequences in May 2003.