Using bioinformatics tools for the sequence analysis of immunoglobulins and T cell receptors

The huge potential repertoire of 10(12) immunoglobulins and 10(12) T cell receptors per individual results from complex mechanisms of combinatorial diversity between the variable (V), diversity (D), and junction (J) genes, nucleotide deletions and insertions (N-diversity) at the junctions and, for the immunoglobulins, somatic hypermutations. The accurate analysis of rearranged immunoglobulin and T cell receptor sequences, and the annotation of the junctions, therefore represent a huge challenge. The IMGT Scientific chart rules, based on the IMGT-ONTOLOGY concepts, were the prerequisites for the implementation of the IMGT/V-QUEST and IMGT/JunctionAnalysis tools. IMGT/V-QUEST analyzes germline V and rearranged V-J or V-D-J nucleotide sequences. IMGT/JunctionAnalysis is the first tool that automatically analyzes the complex junctions in detail. These interactive tools are easy to use and freely available on the Web (http://imgt.cines.fr), either separately or integrated.