IMGT/Junction Analysis: the first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs

Motivation: 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/Junction Analysis 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.