UCSC Genome Browser REST API

Name: UCSC Genome Browser REST API
Brand: UCSC Genome Browser REST API
Availability: InStock

★ Only Publicly Available OpenAPI DocumentData EnrichmentData Transformationnone12 EndpointsREST

For Agents

Query UCSC Genome Browser data — assemblies, tracks, sequences, and chromosome metadata — directly from a bioinformatics pipeline or research agent.

Connect the UCSC Genome Browser REST API to your agent

Jentic One is a self-hosted execution layer for AI agents. It lets your agent call the UCSC Genome Browser REST API, or any other public or private API you need. You set the rules, the agent never sees your credentials, and every call is logged.

Install Jentic One Beta (Self-Hosted)

Jentic One Host machine

# On the machine that will host your Jentic One instance:
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh

Agent machine

# On the machine where your agent runs (keep this separate from the instance):
curl -fsSL https://raw.githubusercontent.com/jentic/jentic-one/main/tools/install.sh | sh
jentic register       # connects your agent to your Jentic One instance

Jentic One is in public beta. The setup above keeps your agent separate from the instance, which is what you want before using real credentials: an agent running as the same OS user as Jentic One can read its stored keys directly. Just evaluating? A single local install is fine to start. See the secure deployment guide for the tiers.

Capabilities

What an agent can do with UCSC Genome Browser REST API.

Find genomes by name or accession across UCSC, GenArk, and public hub collections

List the annotation tracks available for a specific assembly with their schemas

Retrieve chromosome lists and lengths for a target genome

Pull DNA sequence for a specified region from an assembly

GET STARTED

Start building with UCSC Genome Browser REST API

Explore with Jentic

View OpenAPI Document

Jentic publishes the only available OpenAPI specification for UCSC Genome Browser REST API, keeping it validated and agent-ready. The UCSC Genome Browser REST API exposes the institute's reference genome database to programmatic clients, covering genome assemblies, public hubs, GenArk genomes, annotation tracks, chromosome lists, sequence retrieval, and a free-text search across track schemas. It is widely used by bioinformatics pipelines that need authoritative coordinates and sequence data without scraping the browser UI. The endpoints are read-only and do not require authentication.

Use Cases

Patterns agents use UCSC Genome Browser REST API for, with concrete tasks.

★ Variant Annotation Pipeline

Bioinformatics pipelines annotating sequencing variants need fast access to reference sequence and gene-prediction tracks. The /getData/sequence and /getData/track endpoints return the surrounding sequence context and feature overlaps for each variant call, letting the pipeline classify a variant as coding, regulatory, or intergenic without standing up a local UCSC mirror.

For each variant in a VCF, call /getData/sequence around the position and /getData/track for the gene-prediction track to record the feature overlap

Genome Browser Embedding

Research portals and lab websites embed lightweight genome views without hosting a full UCSC mirror. The /list/tracks and /list/chromosomes endpoints provide the structural metadata to render a track selector, and /getData/track returns the visible region's data on demand for client-side rendering.

List tracks for hg38 via /list/tracks, render the track selector, then call /getData/track for the user's selected region

Comparative Genomics Lookup

Researchers comparing assemblies across species need quick access to chromosome counts, lengths, and available tracks. /list/ucscGenomes and /list/genarkGenomes enumerate the full catalogue, /list/chromosomes returns assembly structure, and /findGenome resolves species names to assembly IDs — useful for building comparative-genomics dashboards over many organisms.

Resolve species 'Mus musculus' via /findGenome, list its chromosomes via /list/chromosomes, and add the assembly to the comparative dashboard

AI Agent Bioinformatics Assistant

An AI agent answering genomics questions can ground its replies in UCSC's authoritative data. Through Jentic the agent searches for 'get DNA sequence', loads the schema for /getData/sequence, and executes the call. Because the API is open, no credentials are needed — Jentic still routes the request and validates the schema.

Search Jentic for 'get DNA sequence from UCSC', execute /getData/sequence for chr1 100000-100100 in hg38, and return the sequence to the chat thread

Key Endpoints

12 endpoints — jentic publishes the only available openapi specification for ucsc genome browser rest api, keeping it validated and agent-ready.

METHOD

PATH

DESCRIPTION

GET

/findGenome

Find a genome by name or accession

GET

/list/ucscGenomes

List UCSC-hosted genome assemblies

GET

/list/tracks

List annotation tracks for an assembly

GET

/list/chromosomes

List chromosomes and lengths for an assembly

GET

/getData/sequence

Retrieve DNA sequence for a region

GET

/getData/track

Retrieve track data for a region

GET

/search

Search across track schemas

GET

/findGenome

Find a genome by name or accession

GET

/list/ucscGenomes

List UCSC-hosted genome assemblies

GET

/list/tracks

List annotation tracks for an assembly

GET

/list/chromosomes

List chromosomes and lengths for an assembly

GET

/getData/sequence

Retrieve DNA sequence for a region

Why Jentic?

Three things that make agents converge on Jentic-routed access.

Credential isolation

The UCSC Genome Browser API does not require credentials, so no secrets are stored. Jentic still routes the agent's call through its execution layer for validation, retry handling, and consistent observability across authenticated and unauthenticated APIs.

Intent-based discovery

Agents search by intent ('get DNA sequence' or 'list genome tracks') and Jentic returns the matching UCSC operation with its parameter schema — chrom, start, end, genome — so the agent calls the right endpoint without browsing UCSC docs.

Time to first call

Direct UCSC integration: a few hours to wire each endpoint and handle the parameter conventions per call. Through Jentic: under 15 minutes — search, load, execute.

FAQs

Specific to using UCSC Genome Browser REST API through Jentic.

Why is there no official OpenAPI spec for UCSC Genome Browser REST API?

UCSC documents the REST API on its help pages but does not publish an OpenAPI specification. Jentic generates and maintains this spec so that AI agents and developers can call UCSC Genome Browser REST API via structured tooling. It is validated against the live API and kept up to date. Get started at https://app.jentic.com/sign-up.

What authentication does the UCSC Genome Browser API use?

The API is open and requires no authentication. Requests go directly to api.genome.ucsc.edu without an API key, token, or signed header. UCSC asks consumers to be considerate with request volume — heavy programmatic users should consider mirroring track data locally.

Can I retrieve raw DNA sequence with this API?

Yes. GET /getData/sequence returns the DNA sequence for a specified region (genome, chromosome, start, end). Combine with /list/chromosomes to confirm valid chromosome names and lengths before requesting a slice.

What are the rate limits for the UCSC Genome Browser API?

The OpenAPI spec does not declare explicit limits. UCSC operates a shared public service — for production-scale workloads, batch your queries, cache results, and consider running a local UCSC mirror or downloading the relevant assembly files directly.

How do I look up a gene track for a region through Jentic?

Run pip install jentic, search Jentic for 'get UCSC track data', and call /getData/track with genome, track name, chrom, start, and end. The response includes the feature records overlapping the region for downstream annotation.

Is the UCSC Genome Browser REST API free?

Yes. The API is provided free by UCSC as part of the public Genome Browser project. No paid tier exists — usage is governed by community-considerate request patterns rather than a billing relationship.