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UCSC Genomic Data

The UCSC Genome Browser is a widely-used bioinformatics tool providing access to genomic data, sequence information, and annotation tracks for hundreds of organisms. The REST API provides programmatic access to genome assemblies, DNA sequences, annotation tracks, and track hubs. No authentication is required; rate limiting of one request per second is recommended. Data is returned in JSON format.

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APIs

UCSC Genome Browser REST API

REST API providing programmatic access to the UCSC Genome Browser's genomic data, including genome assemblies, DNA sequences, annotation tracks, and track hubs. All endpoints us...

Collections

UCSC Genome Browser REST API

OPEN

Pricing Plans

Ucsc Genomic Data Plans Pricing

3 plans

PLANS

Rate Limits

Ucsc Genomic Data Rate Limits

5 limits

RATE LIMITS

FinOps

Ucsc Genomic Data Finops

FINOPS

Semantic Vocabularies

Ucsc Genomic Data Context

5 classes · 16 properties

JSON-LD

API Governance Rules

UCSC Genomic Data API Rules

6 rules · 1 errors 5 warnings

SPECTRAL

JSON Structure

Ucsc Genomic Data Structure

0 properties

JSON STRUCTURE

Example Payloads

Ucsc Get Dna Sequence Example

2 fields

EXAMPLE

Ucsc List Tracks Example

2 fields

EXAMPLE

Resources

👥
GitHubOrganization
GitHubOrganization
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LinkedIn
LinkedIn

Sources

Raw ↑ 
opencollection: 1.0.0
info:
  name: UCSC Genome Browser REST API
  version: 1.0.0
items:
- info:
    name: Genomes
    type: folder
  items:
  - info:
      name: Find Genome
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/findGenome
      params:
      - name: q
        value: ''
        type: query
        description: Search query string (genome name, accession, or keyword).
      - name: browser
        value: ''
        type: query
        description: Filter by browser name.
      - name: year
        value: ''
        type: query
        description: Filter assemblies by year.
      - name: category
        value: ''
        type: query
        description: Filter by category.
      - name: status
        value: ''
        type: query
        description: Filter by assembly status.
      - name: level
        value: ''
        type: query
        description: Filter by assembly level.
      - name: statsOnly
        value: ''
        type: query
        description: Return only statistics if set to 1.
      - name: maxItemsOutput
        value: ''
        type: query
        description: Maximum number of items to return.
    docs: Search for genomes by name, accession number, or keywords across NCBI and UCSC assemblies.
  - info:
      name: List UCSC Genomes
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/list/ucscGenomes
    docs: Returns all genome database assemblies available in the UCSC Genome Browser.
  - info:
      name: List GenArk Genomes
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/list/genarkGenomes
      params:
      - name: genome
        value: ''
        type: query
        description: Filter by genome assembly name.
      - name: maxItemsOutput
        value: ''
        type: query
        description: Maximum number of items to return.
    docs: Returns genome assemblies from the GenArk repository.
  - info:
      name: List Genome Files
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/list/files
      params:
      - name: genome
        value: ''
        type: query
        description: Genome assembly identifier (e.g., hg38, mm39).
      - name: format
        value: ''
        type: query
        description: File format filter (e.g., bigBed, bigWig).
      - name: maxItemsOutput
        value: ''
        type: query
        description: Maximum number of files to return.
    docs: Returns download files available for a genome assembly.
  - info:
      name: List Chromosomes
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/list/chromosomes
      params:
      - name: genome
        value: ''
        type: query
        description: Genome assembly identifier (e.g., hg38, mm39).
      - name: hubUrl
        value: ''
        type: query
        description: URL of the hub.txt file for a track hub.
      - name: track
        value: ''
        type: query
        description: Filter chromosomes by a specific track.
    docs: Returns the list of chromosomes in a genome assembly or specific track.
- info:
    name: Hubs
    type: folder
  items:
  - info:
      name: List Public Hubs
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/list/publicHubs
    docs: Returns all publicly available track hubs registered with UCSC.
  - info:
      name: List Hub Genomes
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/list/hubGenomes
      params:
      - name: hubUrl
        value: ''
        type: query
        description: URL of the hub.txt file for the track hub.
    docs: Returns the list of genomes available in a specific track hub.
- info:
    name: Tracks
    type: folder
  items:
  - info:
      name: List Tracks
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/list/tracks
      params:
      - name: genome
        value: ''
        type: query
        description: Genome assembly identifier (e.g., hg38, mm39). Required unless hubUrl is provided.
      - name: hubUrl
        value: ''
        type: query
        description: URL of the hub.txt file for a track hub.
      - name: trackLeavesOnly
        value: ''
        type: query
        description: Set to 1 to return only leaf tracks (hide composite containers).
    docs: Returns all data tracks available for a given genome assembly or hub.
  - info:
      name: Get Track Schema
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/list/schema
      params:
      - name: genome
        value: ''
        type: query
        description: Genome assembly identifier (e.g., hg38, mm39).
      - name: track
        value: ''
        type: query
        description: Track name to return schema for.
      - name: hubUrl
        value: ''
        type: query
        description: URL of the hub.txt file for a track hub.
    docs: Returns the schema and field definitions for a specific annotation track.
  - info:
      name: Get Track Data
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/getData/track
      params:
      - name: genome
        value: ''
        type: query
        description: Genome assembly identifier (e.g., hg38, mm39).
      - name: track
        value: ''
        type: query
        description: Track name to retrieve data from.
      - name: chrom
        value: ''
        type: query
        description: Chromosome to retrieve data for.
      - name: start
        value: ''
        type: query
        description: Start position (0-based).
      - name: end
        value: ''
        type: query
        description: End position (1-based).
      - name: hubUrl
        value: ''
        type: query
        description: URL of the hub.txt file for a track hub.
      - name: maxItemsOutput
        value: ''
        type: query
        description: Maximum number of annotation items to return.
      - name: jsonOutputArrays
        value: ''
        type: query
        description: Set to 1 to format output as JSON arrays instead of objects.
    docs: Retrieves annotation data from a specific track for a genomic region.
- info:
    name: Sequences
    type: folder
  items:
  - info:
      name: Get DNA Sequence
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/getData/sequence
      params:
      - name: genome
        value: ''
        type: query
        description: Genome assembly identifier (e.g., hg38, mm39).
      - name: chrom
        value: ''
        type: query
        description: Chromosome identifier (e.g., chr1, chrM).
      - name: start
        value: ''
        type: query
        description: Start position (0-based, half-open coordinates).
      - name: end
        value: ''
        type: query
        description: End position (1-based, half-open coordinates).
      - name: revComp
        value: ''
        type: query
        description: Set to 1 to return the reverse complement sequence.
      - name: hubUrl
        value: ''
        type: query
        description: URL of the hub.txt file for a sequence hub.
    docs: Retrieves a DNA sequence from a genome assembly for a specified genomic region.
- info:
    name: Search
    type: folder
  items:
  - info:
      name: Search Genome Browser
      type: http
    http:
      method: GET
      url: https://api.genome.ucsc.edu/search
      params:
      - name: search
        value: ''
        type: query
        description: Search query string.
      - name: genome
        value: ''
        type: query
        description: Genome assembly identifier to search within.
      - name: categories
        value: ''
        type: query
        description: Restrict search scope (e.g., helpDocs, publicHubs, trackDb).
    docs: Searches across track data, names, and descriptions in the Genome Browser.
bundled: true