UCSC Genome Browser MCP Server

Instructions

Implementation Reference

• ucsc-genome-mcp.py:411-421 (handler)

  The execution handler for the get_sequence tool. It extracts parameters from the tool arguments, builds the UCSC API URL for the /getData/sequence endpoint, and fetches the DNA sequence data.

  elif name == "get_sequence":
      params = {
          "genome": arguments["genome"],
          "chrom": arguments["chrom"],
          "start": arguments.get("start"),
          "end": arguments.get("end"),
          "hubUrl": arguments.get("hub_url"),
          "revComp": 1 if arguments.get("reverse_complement") else None
      }
      url = build_api_url("/getData/sequence", params)
      result = await make_api_request(url)

• ucsc-genome-mcp.py:233-266 (registration)

  The registration of the get_sequence tool in the list_tools() function, defining its name, description, and input schema for MCP.

  Tool(
      name="get_sequence",
      description="Retrieve DNA sequence from a specified genome assembly. Can retrieve entire chromosome or specific coordinates.",
      inputSchema={
          "type": "object",
          "properties": {
              "genome": {
                  "type": "string",
                  "description": "Genome assembly name (e.g., 'hg38')"
              },
              "chrom": {
                  "type": "string",
                  "description": "Chromosome name (e.g., 'chr1', 'chrM')"
              },
              "start": {
                  "type": "integer",
                  "description": "Start coordinate (0-based, optional, requires end)"
              },
              "end": {
                  "type": "integer",
                  "description": "End coordinate (1-based, optional, requires start)"
              },
              "hub_url": {
                  "type": "string",
                  "description": "URL of assembly hub (optional)"
              },
              "reverse_complement": {
                  "type": "boolean",
                  "description": "Return reverse complement of sequence"
              }
          },
          "required": ["genome", "chrom"]
      }
  ),

• ucsc-genome-mcp.py:236-265 (schema)

  The input schema definition for the get_sequence tool, specifying parameters like genome, chrom, start, end, etc.

  inputSchema={
      "type": "object",
      "properties": {
          "genome": {
              "type": "string",
              "description": "Genome assembly name (e.g., 'hg38')"
          },
          "chrom": {
              "type": "string",
              "description": "Chromosome name (e.g., 'chr1', 'chrM')"
          },
          "start": {
              "type": "integer",
              "description": "Start coordinate (0-based, optional, requires end)"
          },
          "end": {
              "type": "integer",
              "description": "End coordinate (1-based, optional, requires start)"
          },
          "hub_url": {
              "type": "string",
              "description": "URL of assembly hub (optional)"
          },
          "reverse_complement": {
              "type": "boolean",
              "description": "Return reverse complement of sequence"
          }
      },
      "required": ["genome", "chrom"]
  }

• ucsc-genome-mcp.py:27-37 (helper)

  Helper function build_api_url used by get_sequence handler to construct the UCSC API request URL with semicolon-separated parameters.

  def build_api_url(endpoint: str, params: dict[str, Any]) -> str:
      """Build the complete API URL with parameters."""
      # Filter out None values
      filtered_params = {k: v for k, v in params.items() if v is not None}
      
      # Convert parameters to URL format (using semicolons as per UCSC API spec)
      if filtered_params:
          param_str = ";".join(f"{k}={v}" for k, v in filtered_params.items())
          return f"{BASE_URL}{endpoint}?{param_str}"
      return f"{BASE_URL}{endpoint}"

• ucsc-genome-mcp.py:39-45 (helper)

  Helper function make_api_request used by get_sequence handler to perform the asynchronous HTTP GET request to the UCSC API and parse JSON response.

  async def make_api_request(url: str) -> dict[str, Any]:
      """Make an HTTP request to the UCSC API and return JSON response."""
      async with httpx.AsyncClient(timeout=30.0) as client:
          response = await client.get(url)
          response.raise_for_status()
          return response.json()