IMGT V-QUEST

IMGT V-QUEST analyzes rearranged immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences to identify V, D and J genes and alleles, detect V-region mutations and indels, and characterize junctions for immunogenetic and structural analyses using IMGT reference data and IMGT-ONTOLOGY concepts.

Key Features:

• Sequence alignment and germline identification: Aligns input sequences with germline IG and TR gene and allele sequences from the IMGT reference directory to identify V, D and J genes and alleles.
• Mutation identification and indel annotation: Detects V-region mutations, locates mutation hot spots relative to the closest germline V gene, and identifies insertions and deletions using IMGT unique numbering.
• Junction analysis: Integrates with IMGT/JunctionAnalysis to examine V-J and V-D-J junctions and recombination features.
• Graphical representation: Generates two-dimensional IMGT Collier de Perles representations of variable regions for structural visualization.
• Phylogenetic analysis: Interacts with IMGT/PhyloGene to construct phylogenetic trees for evolutionary studies of immune genes.
• Batch processing: Supports batch analysis of up to 50 sequences simultaneously.
• Advanced parameterization: Provides advanced parameters to modify analysis settings and defaults.
• Species coverage: Supports human and mouse fully, with partial support for non-human primates, sheep, chondrichthyes, and teleostei.

Scientific Applications:

• Basic immunology and repertoire analysis: Characterizes V(D)J rearrangements and somatic mutation patterns in IG and TR repertoires.
• Clinical mutation analysis: Supports mutation profiling relevant to hematological malignancies such as leukemia and lymphoma.
• Antibody engineering and humanization: Aids therapeutic antibody and fusion protein development and analysis, interfacing with IMGT/mAb-DB.
• Veterinary and comparative immunogenetics: Enables immunogenetic analysis across multiple species including livestock and non-model organisms.

Methodology:

Applies IMGT-ONTOLOGY-based gene identification, alignment of input sequences to the IMGT reference directory of germline IG and TR gene and allele sequences, IMGT unique numbering for indel and positional annotation, integration with IMGT/JunctionAnalysis for junction characterization and with IMGT/PhyloGene for phylogenetic construction, and generation of IMGT Collier de Perles two-dimensional representations.