hlydecker/ucsc-genome-mcp

Overview

An MCP server that provides a programmatic interface to the UCSC Genome Browser API. It enables AI agents and tools to query genomic data through the Model Context Protocol, using Python to translate requests into API calls.

Best for

Best for
Developers building AI agents or tools that need to query genomic data from UCSC

Use cases

• Fetching genomic sequences and annotations for analysis
• Integrating UCSC genome data into AI-driven research workflows
• Automating retrieval of gene tracks and regulatory features

How to use

Install

pip install -e .

Tools exposed

• find_genome
• list_public_hubs
• list_ucsc_genomes
• list_genark_genomes
• list_hub_genomes
• list_files
• list_tracks
• list_chromosomes
• list_schema
• get_sequence
• get_track_data
• search_genome

Tested with

Claude Desktop

Example client config

{\n  "mcpServers": {\n    "ucsc-genome-browser": {\n      "command": "/Users/You/.local/bin/uv",\n      "args": [\n        "--directory",\n        "/Users/Path/To/Repository/ucsc-genome-mcp",\n        "run",\n        "ucsc-genome-mcp.py"\n      ],\n      "env": {},\n      "metadata": {\n        "description": "UCSC Genome Browser API",\n        "version": "1.0.0"\n      }\n    }\n  }\n}

Notes

An MCP server that provides a programmatic interface to the UCSC Genome Browser API. It enables AI agents and tools to query genomic data through the Model Context Protocol, using Python to translate requests into API calls.

5 stars on GitHub. Last updated 2025-11-13. Licensed MIT.

Use cases

• Fetching genomic sequences and annotations for analysis
• Integrating UCSC genome data into AI-driven research workflows
• Automating retrieval of gene tracks and regulatory features

Pros

• Simplifies access to UCSC Genome Browser data via the MCP standard
• Written in Python, easy to extend or embed in existing projects
• Open source with a permissive license for customization

Cons

• Very early stage with only 5 GitHub stars, limited community validation
• Documentation and error handling may be sparse
• Depends on UCSC API availability and rate limits

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