UCSC Genome Browser FAQs

Question 1

What is the UCSC Genome Browser API tool?

Accepted Answer

The UCSC Genome Browser API tool is a Model Context Protocol (MCP) server that provides comprehensive access to the UCSC Genome Browser's vast genomic datasets, enabling LLM applications to query sequences, tracks, and metadata programmatically.

Question 2

What types of genomic data can I access through this API?

Accepted Answer

You can access a wide range of genomic data, including DNA sequences, track data (genes, variants, annotations), genome listings, public track hubs, and chromosome information. It supports advanced queries for specific regions and reverse complements.

Question 3

How do LLMs utilize this UCSC Genome Browser API?

Accepted Answer

LLMs can use this API to power genomic research by querying gene locations, performing variant analysis, conducting comparative genomics, retrieving sequences for analysis, and discovering available datasets, making complex biological queries accessible.

Question 4

Does it support accessing data from external sources or specific hubs?

Accepted Answer

Yes, the tool supports integration with track hubs, allowing LLMs to list and query genomes and track data from specific external assembly hubs, expanding the scope of accessible genomic information beyond UCSC's core datasets.

Question 5

How do I integrate this API into my LLM application?

Accepted Answer

The tool runs as an MCP server, communicating over stdio. It can be installed via Python's pip and configured with LLM platforms like Claude Desktop by specifying the command and repository path in the application's configuration file.

UCSC Genome Browser

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