UCSC Genome Browser MCP Server
Server Configuration
Describes the environment variables required to run the server.
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Instructions
Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.
This server publishes no instructions, or was last inspected before Glama recorded them.
Capabilities
Server capabilities have not been inspected yet.
Tools
Functions exposed to the LLM to take actions
| Name | Description |
|---|---|
| find_genomeB | Search for a genome in the UCSC browser using a search string. Supports advanced search with +word (force inclusion), -word (exclusion), and word* (wildcard). |
| list_public_hubsB | List all available public track hubs in the UCSC Genome Browser. |
| list_ucsc_genomesA | List all UCSC Genome Browser database genomes available on the database host. |
| list_genark_genomesB | List UCSC Genome Browser database genomes from assembly hub host (GenArk). Can also test for existence of a specific genome. |
| list_hub_genomesC | List all genomes available in a specified track or assembly hub. |
| list_filesB | List download files available for a specified UCSC genome assembly. |
| list_tracksC | List all data tracks available in a specified hub or UCSC database genome. |
| list_chromosomesB | List chromosomes in an assembly hub, track hub, or UCSC database genome. Optionally filter by specific track. |
| list_schemaB | List the schema (field definitions) for a specified data track. |
| get_sequenceB | Retrieve DNA sequence from a specified genome assembly. Can retrieve entire chromosome or specific coordinates. |
| get_track_dataB | Retrieve data from a specified track in a hub or UCSC database genome. Can be filtered by chromosome and coordinates. |
| search_genomeC | Search for matches within a UCSC Genome Browser genome assembly across tracks, help docs, and public hubs. |
Prompts
Interactive templates invoked by user choice
| Name | Description |
|---|---|
No prompts | |
Resources
Contextual data attached and managed by the client
| Name | Description |
|---|---|
No resources | |
TDQS
Scored across 12 tools
Most tools have distinct purposes, but there is some overlap between 'find_genome' and 'search_genome'—both involve searching genomes, which could cause confusion. The other tools target specific resources like sequences, tracks, chromosomes, files, and hubs with clear boundaries.
All tool names follow a consistent verb_noun pattern using snake_case, such as 'find_genome', 'get_sequence', and 'list_tracks'. This predictability makes it easy for agents to understand and use the toolset without confusion.
With 12 tools, the count is well-suited for the UCSC Genome Browser domain, covering key operations like searching, retrieving data, and listing resources. Each tool serves a specific function without redundancy, making the set comprehensive yet manageable.
The toolset provides strong coverage for browsing and retrieving genomic data, including search, sequence access, track management, and hub listings. A minor gap is the lack of tools for modifying or updating data, but this aligns with the server's likely read-only focus on the UCSC Browser.