UCSC Genome Browser MCP Server
A Model Context Protocol (MCP) server that provides comprehensive access to the UCSC Genome Browser API. This server enables LLM applications to query genomic data, sequences, tracks, and metadata from the UCSC Genome Browser.
Features
This MCP server exposes 12 tools that cover all major UCSC Genome Browser API endpoints:
Listing & Discovery Tools
- find_genome - Search for genomes using keywords, accession IDs, or organism names
- list_public_hubs - List all available public track hubs
- list_ucsc_genomes - List all UCSC database genomes
- list_genark_genomes - List GenArk assembly hub genomes
- list_hub_genomes - List genomes from a specific hub
- list_files - List downloadable files for a genome
- list_tracks - List data tracks in a genome or hub
- list_chromosomes - List chromosomes in a genome or track
- list_schema - Get schema/field definitions for a track
Data Retrieval Tools
- get_sequence - Retrieve DNA sequences from genomes
- get_track_data - Get track data (genes, variants, annotations, etc.)
- search_genome - Search within a genome assembly
