Motivation: To create the enormous diversity of 1012 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.

Availability: IMGT/JunctionAnalysis is available from the IMGT Home page at http://imgt. cines. fr Contact: lefranc@ ligm. igh. cnrs. fr