IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis

Abstract

IMGT/V-QUEST is the highly customized and integrated system for the standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. IMGT/V-QUEST identifies the variable (V), diversity (D) and joining (J) genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. New functionalities were added through a complete rewrite in Java. IMGT/V-QUEST analyses batches of sequences (up to 50) in a single run. IMGT/V-QUEST describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST can detect insertions and deletions in the submitted sequences by reference to the IMGT unique numbering. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions, and IMGT/Automat for a full V-J- and V-D-J-REGION annotation. IMGT/V-QUEST displays, in 'Detailed view', the results and alignments for each submitted sequence individually and, in 'Synthesis view', the alignments of the sequences that, in a given run, express the same V gene and allele. The 'Advanced parameters' allow to modify default parameters used by IMGT/V-QUEST and IMGT/JunctionAnalysis according to the users' interest. IMGT/V-QUEST is freely available for academic research at http://imgt.cines.fr.

Figure 1.

The customizable parameters for an IMGT/V-QUEST search. ‘Selection for results display’ allows the users to select the types of results to be displayed (14 for ‘Detailed view’, and 8 for ‘Synthesis view’). The ‘Advanced parameters’ allow the users to modify the default values.

Figure 2.

IMGT/V-QUEST output. (A) ‘Result summary’ of ‘Detailed view’. The note (a) represents a warning indicating that there is another possibility for the choice of the J-GENE, the criterion for that choice being between parentheses. In the case of an unproductive sequence due to an out-of-frame junction, the CDR3-IMGT length cannot be determined and is indicated by an ‘X’. The symbol ‘#’ indicates a frameshift. (B) ‘Summary table’ of ‘Synthesis view’. The note (a) represents a warning indicating that there are other possibilities for the results.

Figure 3.

IMGT/JunctionAnalysis translation of ‘Synthesis view’. Results are given per locus, here five IGH sequences are shown. Amino acids of the JUNCTIONs are colored according to the 11 IMGT AA physicochemical classes (12). Underlined nt and AA are mutated compared with the closest germline 3′V-REGION, D-REGION and 5′J-REGION of each JUNCTION.