title: IMGT/JunctionAnalysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs.
abstract: BACKGROUND
  To create the enormous diversity of 10(12) immunoglobulins (IG) and T cell receptors (TR) per individual, very complex mechanisms occur at the DNA level: the combinatorial diversity results from the junction of the variable (V), diversity (D) and joining (J) genes; the N-diversity represents the addition at random of nucleotides not encoded in the genome; and somatic hypermutations occur in IG rearranged sequences. The accurate annotation of the junction between V, D, J genes in rearranged IG and TR sequences represents therefore a huge challenge by its uniqueness and complexity. We developed IMGT/JunctionAnalysis to analyse automatically in detail the IG and TR junctions, according to the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY concepts.
  
  
  RESULTS
  IMGT/JunctionAnalysis is the first tool for the detailed analysis of the IG and TR complex V-J and V-D-J JUNCTION(s). It delimits, at the nucleotide level, the genes resulting from the combinatorial diversity. It identifies accurately the D genes in the junctions of IG heavy (IGH), TR beta (TRB) and delta (TRD) chains. It delimits the palindromic P-REGION(s) and the N-REGION(s) resulting from the N-diversity. It evaluates the number of somatic hypermutations for each gene, within the JUNCTION. IMGT/JunctionAnalysis is capable of analysing, in a single run, an unlimited number of junctions from the same species (currently human or mouse) and from the same locus.
  
  
  BACKGROUND
  IMGT/JunctionAnalysis is available from the IMGT Home page at http://imgt.cines.fr
authors.affiliation: Laboratoire d'ImmunoGénétique Moléculaire LIGM, Université Montpellier II, UPR CNRS 1142, Institut de Génétique Humaine IGH, Montpellier Cedex 5, France.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Yousfi Monod
authors.forename: Véronique
authors.initials: V
authors.lastname: Giudicelli
authors.forename: Denys
authors.initials: D
authors.lastname: Chaume
authors.forename: Marie-Paule
authors.initials: MP
authors.lastname: Lefranc
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D015329:Gene Rearrangement, T-Lymphocyte; D005803:Genes, Immunoglobulin; D014644:Genetic Variation / Q000235:genetics*; D007133:Immunoglobulin Joining Region / Q000235:genetics*; D007136:Immunoglobulins / Q000235:genetics*; D008969:Molecular Sequence Data; D011948:Receptors, Antigen, T-Cell / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
chemical_list: D007133:Immunoglobulin Joining Region; D007136:Immunoglobulins; D011948:Receptors, Antigen, T-Cell