UCSC Genome Browser MCP Server

Instructions

Implementation Reference

• ucsc-genome-mcp.py:437-445 (handler)

  Executes the search_genome tool by building parameters for the UCSC API /search endpoint (search term, genome, optional categories) and fetching the results via make_api_request.
  elif name == "search_genome": params = { "search": arguments["search"], "genome": arguments["genome"], "categories": arguments.get("categories") } url = build_api_url("/search", params) result = await make_api_request(url)
• ucsc-genome-mcp.py:309-331 (schema)

  Defines the Tool schema for search_genome, including input parameters: search (required string), genome (required string), categories (optional enum: helpDocs, publicHubs, trackDb).
  Tool( name="search_genome", description="Search for matches within a UCSC Genome Browser genome assembly across tracks, help docs, and public hubs.", inputSchema={ "type": "object", "properties": { "search": { "type": "string", "description": "Search term" }, "genome": { "type": "string", "description": "Genome assembly to search in" }, "categories": { "type": "string", "enum": ["helpDocs", "publicHubs", "trackDb"], "description": "Restrict search to specific categories" } }, "required": ["search", "genome"] } )
• ucsc-genome-mcp.py:47-332 (registration)

  Registers the search_genome tool within the list_tools() function returned by the @app.list_tools() decorator, making it available to the MCP server.
  @app.list_tools() async def list_tools() -> list[Tool]: """List all available tools for UCSC Genome Browser API.""" return [ Tool( name="find_genome", description="Search for a genome in the UCSC browser using a search string. Supports advanced search with +word (force inclusion), -word (exclusion), and word* (wildcard).", inputSchema={ "type": "object", "properties": { "query": { "type": "string", "description": "Search string to find genomes (e.g., 'dog', 'GRCh38', 'GCF_028858775.2')" }, "browser": { "type": "string", "enum": ["mustExist", "mayExist", "notExist"], "description": "Filter by browser availability (default: mustExist)" }, "stats_only": { "type": "boolean", "description": "Only show statistics about search results" }, "year": { "type": "integer", "description": "Filter results by year" }, "category": { "type": "string", "enum": ["reference", "representative"], "description": "Filter by NCBI category" }, "status": { "type": "string", "enum": ["reference", "representative"], "description": "Filter by NCBI status" }, "level": { "type": "string", "enum": ["complete", "chromosome", "scaffold", "contig"], "description": "Filter by NCBI assembly level" }, "max_items": { "type": "integer", "description": "Maximum number of items to return (default: 1000000, use -1 for max)" } }, "required": ["query"] } ), Tool( name="list_public_hubs", description="List all available public track hubs in the UCSC Genome Browser.", inputSchema={ "type": "object", "properties": {} } ), Tool( name="list_ucsc_genomes", description="List all UCSC Genome Browser database genomes available on the database host.", inputSchema={ "type": "object", "properties": {} } ), Tool( name="list_genark_genomes", description="List UCSC Genome Browser database genomes from assembly hub host (GenArk). Can also test for existence of a specific genome.", inputSchema={ "type": "object", "properties": { "genome": { "type": "string", "description": "Specific genome to test for existence (optional)" }, "max_items": { "type": "integer", "description": "Maximum number of items to return (default: 1000000)" } } } ), Tool( name="list_hub_genomes", description="List all genomes available in a specified track or assembly hub.", inputSchema={ "type": "object", "properties": { "hub_url": { "type": "string", "description": "URL of the track hub or assembly hub" } }, "required": ["hub_url"] } ), Tool( name="list_files", description="List download files available for a specified UCSC genome assembly.", inputSchema={ "type": "object", "properties": { "genome": { "type": "string", "description": "Genome assembly name (e.g., 'hg38', 'mm10')" }, "format": { "type": "string", "enum": ["json", "text"], "description": "Output format (default: json)" }, "max_items": { "type": "integer", "description": "Maximum number of items to return" } }, "required": ["genome"] } ), Tool( name="list_tracks", description="List all data tracks available in a specified hub or UCSC database genome.", inputSchema={ "type": "object", "properties": { "genome": { "type": "string", "description": "Genome assembly name" }, "hub_url": { "type": "string", "description": "URL of track/assembly hub (optional, required with genome for hub tracks)" }, "track_leaves_only": { "type": "boolean", "description": "Only show tracks without composite container information" } }, "required": ["genome"] } ), Tool( name="list_chromosomes", description="List chromosomes in an assembly hub, track hub, or UCSC database genome. Optionally filter by specific track.", inputSchema={ "type": "object", "properties": { "genome": { "type": "string", "description": "Genome assembly name" }, "hub_url": { "type": "string", "description": "URL of track/assembly hub (optional)" }, "track": { "type": "string", "description": "Specific track name to list chromosomes from (optional)" } }, "required": ["genome"] } ), Tool( name="list_schema", description="List the schema (field definitions) for a specified data track.", inputSchema={ "type": "object", "properties": { "genome": { "type": "string", "description": "Genome assembly name" }, "track": { "type": "string", "description": "Track name" }, "hub_url": { "type": "string", "description": "URL of track/assembly hub (optional)" } }, "required": ["genome", "track"] } ), 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"] } ), Tool( name="get_track_data", description="Retrieve data from a specified track in a hub or UCSC database genome. Can be filtered by chromosome and coordinates.", inputSchema={ "type": "object", "properties": { "genome": { "type": "string", "description": "Genome assembly name" }, "track": { "type": "string", "description": "Track name" }, "chrom": { "type": "string", "description": "Chromosome name (optional)" }, "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 track/assembly hub (optional)" }, "max_items": { "type": "integer", "description": "Maximum number of items to return (default: 1000000)" }, "json_output_arrays": { "type": "boolean", "description": "Return data as JSON arrays instead of objects" } }, "required": ["genome", "track"] } ), Tool( name="search_genome", description="Search for matches within a UCSC Genome Browser genome assembly across tracks, help docs, and public hubs.", inputSchema={ "type": "object", "properties": { "search": { "type": "string", "description": "Search term" }, "genome": { "type": "string", "description": "Genome assembly to search in" }, "categories": { "type": "string", "enum": ["helpDocs", "publicHubs", "trackDb"], "description": "Restrict search to specific categories" } }, "required": ["search", "genome"] } ) ]