VDJdb

VDJdb provides a curated database of T-cell receptor (TCR) sequences linked to cognate antigens to support analysis of TCR specificity and immune recognition.

Key Features:

• Curated TCR–Antigen Reference Dataset: Contains experimentally validated T-cell receptor sequences associated with their cognate antigens.
• Expanded TCR Sequence Collection: Incorporates a substantially increased set of TCR sequences and antigen associations derived from published studies.
• Batch Annotation of TCR Repertoire Data: Supports annotation of TCR repertoire sequencing datasets by matching sequences against database entries.
• TCR Motif Compendium: Provides a curated set of high-confidence TCR sequence motifs derived from bioinformatic motif mining.
• Motif-Based Specificity Analysis: Enables matching of TCR sequences against known motifs to explore potential antigen specificity.

Scientific Applications:

• TCR Specificity Analysis: Identifies antigen specificities associated with T-cell receptor sequences.
• Adaptive Immune Repertoire Research: Analyzes TCR repertoire sequencing datasets to study antigen recognition patterns.
• Machine Learning Model Development: Uses curated TCR motifs and sequence–antigen associations to train TCR specificity prediction models.

Methodology:

VDJdb curates experimentally validated TCR–antigen associations, mines high-confidence TCR sequence motifs using bioinformatic methods, and enables annotation of TCR repertoire sequencing datasets by matching sequences and motifs against the database.