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

By Xavier Brochet, Marie-Paule Lefranc, Véronique Giudicelli. 2008

1,246 citations recorded by the source corpus.

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

Subfields: Immunology

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Citations in the corpus

Nonspecificity in a nonimmune human scFv repertoire (2017, methodology): “IMGT/V-QUEST was used for all sequence alignment and assignment of closest germline V-genes.39 Both input and output libraries were sequenced, and clones with greater than two-fold enrichment over input and p-value less than 0.01 (Student’s t-test, n D 4 replicates) we deemed to be significantly enr”
Flow Cytometry Reveals that H5N1 Vaccination Elicits Cross-Reactive Stem-Directed Antibodies from Multiple Ig Heavy-Chain Lineages (2014, methodology): “Reverse transcription-PCR (RT-PCR) amplification was performed according to the method of Tiller et al. (18), and PCR products were sequenced by Genewiz, Inc. Sequences were analyzed using IGMT/ V-QUEST (19, 20) and grouped into clones in which the complementarity-determining region H3 (CDR-H3) sequ”
Specificity, cross-reactivity, and function of antibodies elicited by Zika virus infection (2016, positive): “The V, D and J genes of the IgH DNA sequences were identified using IMGT database as a reference (45).”
Structure and Function Analysis of an Antibody Recognizing All Influenza A Subtypes (2016, methodology): “The V, D and J genes of the IgH DNA sequences were identified using the IMGT database as a reference (Brochet et al., 2008; Ye et al., 2013).”
IMGT®, the international ImMunoGeneTics information system® (2004, methodology): “IMGT/V-QUEST results comprise, for rearranged sequences, the identiﬁcation of the V, D and J genes and alleles, nucleotide alignments by comparison with the IMGT reference directory, the delimitations of the framework regions (FR-IMGT) and complementarity determining regions (CDR-IMGT) based on the ”
A Special Population of Regulatory T Cells Potentiates Muscle Repair (2013, positive): “Raw sequencing files were filtered for sequence quality, processed in automated fashion, and parsed using IMGT/V-QUEST (Brochet et al., 2008).”
Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires (2016, methodology): “Illumina sequences were quality-filtered and annotated using both the IMGT (60) and National Center for Biotechnology Information IgBlast software (61) with a CDR3 motif identification algorithm (62).”