From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT? standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences

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• 作者：Jér?me Lane (1)
  Patrice Duroux (1)
  Marie-Paule Lefranc (1) (2)
  
• 刊名：BMC Bioinformatics
• 出版年：2010
• 出版时间：December 2010
• 年：2010
• 卷：11
• 期：1
• 全文大小：947KB
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• 作者单位：Jér?me Lane (1)
  Patrice Duroux (1)
  Marie-Paule Lefranc (1) (2)
  
  1. IMGT?, the international ImMunoGeneTics information system?, Université Montpellier 2, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, 34396, Montpellier cedex, 5, France
  2. Institut Universitaire de France, 103 Bd St Michel, 75005, Paris, France
  
• ISSN：1471-2105

文摘

Background The antigen receptors, immunoglobulins (IG) and T cell receptors (TR), are specific molecular components of the adaptive immune response of vertebrates. Their genes are organized in the genome in several loci (7 in humans) that comprise different gene types: variable (V), diversity (D), joining (J) and constant (C) genes. Synthesis of the IG and TR proteins requires rearrangements of V and J, or V, D and J genes at the DNA level, followed by the splicing at the RNA level of the rearranged V-J and V-D-J genes to C genes. Owing to the particularities of IG and TR gene structures related to these molecular mechanisms, conventional bioinformatic software and tools are not adapted to the identification and description of IG and TR genes in large genomic sequences. In order to answer that need, IMGT?, the international ImMunoGeneTics information system?, has developed IMGT/LIGMotif, a tool for IG and TR gene annotation. This tool is based on standardized rules defined in IMGT-ONTOLOGY, the first ontology in immunogenetics and immunoinformatics. Results IMGT/LIGMotif currently annotates human and mouse IG and TR loci in large genomic sequences. The annotation includes gene identification and orientation on DNA strand, description of the V, D and J genes by assigning IMGT? labels, gene functionality, and finally, gene delimitation and cluster assembly. IMGT/LIGMotif analyses sequences up to 2.5 megabase pairs and can analyse them in batch files. Conclusions IMGT/LIGMotif is currently used by the IMGT? biocurators to annotate, in a first step, IG and TR genomic sequences of human and mouse in new haplotypes and those of closely related species, nonhuman primates and rat, respectively. In a next step, and following enrichment of its reference databases, IMGT/LIGMotif will be used to annotate IG and TR of more distantly related vertebrate species. IMGT/LIGMotif is available at http://www.imgt.org/ligmotif/.