IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis

Abstract

IMGT/V-QUEST, for 'V-QUEry and STandardization', is an integrated software program which analyses the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. The extraordinary diversity of the IG and TR repertoires (10(12) antibodies and 10(12) TR per individual) results from several mechanisms at the DNA level: the combinatorial diversity of the variable (V), diversity (D) and joining (J) genes, the N-diversity and, for IG, the somatic mutations. IMGT/V-QUEST identifies the V, D and J genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. IMGT/V-QUEST delimits the structurally important features, frameworks and complementarity-determining regions (the last of these forming the antigen binding site), on the basis of the IMGT unique numbering. The tool localizes the somatic mutations of the IG rearranged sequences. IMGT/V-QUEST also dynamically displays a graphical two-dimensional representation, or IMGT Collier de Perles, of the IG and TR variable regions. Moreover, IMGT/V-QUEST can interact with IMGT/JunctionAnalysis for the detailed description of the V-J and V-D-J junctions, and with IMGT/PhyloGene for the construction of phylogenetic trees. IMGT/V-QUEST is currently available for human and mouse, and partly for non-human primates, sheep, chondrichthyes and teleostei. IMGT/V-QUEST is freely available at http://imgt.cines.fr.

Figure 1

IMGT/V-QUEST results. (A) Alignments for V-GENE, D-GENE and J-GENE, and translation of the JUNCTION. The input sequence is aligned with the closest V, D and J genes and alleles of the IMGT reference directory set. The IMGT/LIGM-DB accession number (identical to the DDBJ/EMBL/GenBank accession number), the IMGT gene name and allele are indicated for each reference sequence. Dashes indicate nucleotide identity. Dots indicate gaps according to the IMGT numbering or nucleotides that are not taken into account for the alignment (16). The JUNCTION extends from the 2nd-CYS (C) at position 104 to J-TRP (W) at position 118. (B) The default option of IMGT/V-QUEST: the alignment for D-GENE is replaced by the results of IMGT/JunctionAnalysis.

Figure 2

IMGT/V-QUEST results. (A) Alignment with the FR–IMGT and the CDR–IMGT delimitations according to the IMGT unique numbering. Dashes indicate nucleotide identity. Dots indicate gaps according to the IMGT numbering or nucleotides that are not taken into account for the alignment (16). Nucleotide differences correspond to somatic mutations. (B) Translation of the input sequence. (C) “Input” V-REGION nucleotide and amino acid sequences in FASTA format with gaps inserted according to the IMGT unique numbering. The formatted nucleotide sequence can be automatically loaded into IMGT/PhyloGene for phylogenetic studies by clicking on the corresponding button (7). (D) IMGT Collier de Perles. Amino acids are shown by one-letter abbreviation. Hydrophobic amino acids and tryptophan (W) found at a given position in more than 50% of analysed IG and TR sequences are shown in blue. All Proline (P) are shown in yellow. The CDR–IMGTs are limited by amino acids shown inside squares.