Cortexa research tool·genomics·Immunology

VDJDB Search Cdr3

Search VDJdb for TCR/BCR CDR3 sequences linked to antigen specificity. Given a CDR3 amino acid sequence, finds matching records with epitope, MHC, V/J gene usage, species, and confidence scores. Supports exact match, fuzzy (Levenshtein distance), and pattern matching. Filter by species (HomoSapiens, MusMusculus, MacacaMulatta) and TCR chain (TRA, TRB). Connects to IMGT gene nomenclature upstream and IEDB epitope data downstream.

Livelast probed 2026-04-30 23:07Z· 95msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 95ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "cdr3": {
      "description": "CDR3 amino acid sequence to search (e.g., 'CASSIRSSYEQYF', 'CAAAASGGSYIPTF')",
      "type": "string"
    },
    "deletions": {
      "description": "Max deletions for fuzzy match (default: 1). Only used with match_type='fuzzy'",
      "type": [
        "integer",
        "null"
      ]
    },
    "gene": {
      "description": "TCR chain filter: TRA (alpha) or TRB (beta)",
      "type": [
        "string",
        "null"
      ]
    },
    "insertions": {
      "description": "Max insertions for fuzzy match (default: 1). Only used with match_type='fuzzy'",
      "type": [
        "integer",
        "null"
      ]
    },
    "match_type": {
      "default": "exact",
      "description": "Match type: 'exact' for exact CDR3 match, 'fuzzy' for Levenshtein distance, 'pattern' for regex pattern",
      "enum": [
        "exact",
        "fuzzy",
        "pattern"
      ],
      "type": "string"
    },
    "operation": {
      "description": "Operation type",
      "enum": [
        "search_cdr3"
      ],
      "type": "string"
    },
    "page": {
      "default": 0,
      "description": "Page number (0-indexed) for paginated results",
      "minimum": 0,
      "type": "integer"
    },
    "page_size": {
      "default": 25,
      "description": "Number of results per page (default: 25, max: 100)",
      "maximum": 100,
      "minimum": 1,
      "type": "integer"
    },
    "species": {
      "description": "Species filter: HomoSapiens, MusMusculus, or MacacaMulatta",
      "type": [
        "string",
        "null"
      ]
    },
    "substitutions": {
      "description": "Max substitutions for fuzzy match (default: 1). Only used with match_type='fuzzy'",
      "type": [
        "integer",
        "null"
      ]
    }
  },
  "required": [
    "operation",
    "cdr3"
  ],
  "type": "object"
}

Examples (1)

Default VDJDB Search Cdr3 call

public-safeinput

{
  "cdr3": "",
  "operation": "",
  "page": 1,
  "page_size": 1
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_VDJDB_search_cdr3
Tool name: VDJDB_search_cdr3
Added: 2026-04-30 22:47Z
Tags: tooluniverse

VDJDB Search Cdr3

Livelast probed 2026-04-30 23:07Z· 95msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "cdr3": { "description": "CDR3 amino acid sequence to search (e.g., 'CASSIRSSYEQYF', 'CAAAASGGSYIPTF')", "type": "string" }, "deletions": { "description": "Max deletions for fuzzy match (default: 1). Only used with match_type='fuzzy'", "type": [ "integer", "null" ] }, "gene": { "description": "TCR chain filter: TRA (alpha) or TRB (beta)", "type": [ "string", "null" ] }, "insertions": { "description": "Max insertions for fuzzy match (default: 1). Only used with match_type='fuzzy'", "type": [ "integer", "null" ] }, "match_type": { "default": "exact", "description": "Match type: 'exact' for exact CDR3 match, 'fuzzy' for Levenshtein distance, 'pattern' for regex pattern", "enum": [ "exact", "fuzzy", "pattern" ], "type": "string" }, "operation": { "description": "Operation type", "enum": [ "search_cdr3" ], "type": "string" }, "page": { "default": 0, "description": "Page number (0-indexed) for paginated results", "minimum": 0, "type": "integer" }, "page_size": { "default": 25, "description": "Number of results per page (default: 25, max: 100)", "maximum": 100, "minimum": 1, "type": "integer" }, "species": { "description": "Species filter: HomoSapiens, MusMusculus, or MacacaMulatta", "type": [ "string", "null" ] }, "substitutions": { "description": "Max substitutions for fuzzy match (default: 1). Only used with match_type='fuzzy'", "type": [ "integer", "null" ] } }, "required": [ "operation", "cdr3" ], "type": "object" }