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JASPAR (Transcription Factor Binding Profiles)

| Endpoint | Description | |----------|-------------| | `/matrix/` | List all TF binding profiles | | `/matrix/{matrix_id}/` | Specific profile (e.g. MA0139.1 for CTCF) | | `/matrix/?tax_id={id}&collection=CORE` | Filter by species + collection | | `/matrix/{id}/?format=jaspar` | Profile in JASPAR format | | `/matrix/{id}/?format=meme` | Profile in MEME format | | `/matrix/{id}/?format=transfac` |

Claude Code Knowledge Pack7/10/2026

Overview

JASPAR (Transcription Factor Binding Profiles)

Base URL

https://jaspar.elixir.no/api/v1/

Auth

No auth required.

Key Endpoints

EndpointDescription
/matrix/List all TF binding profiles
/matrix/{matrix_id}/Specific profile (e.g. MA0139.1 for CTCF)
/matrix/?tax_id={id}&collection=COREFilter by species + collection
/matrix/{id}/?format=jasparProfile in JASPAR format
/matrix/{id}/?format=memeProfile in MEME format
/matrix/{id}/?format=transfacProfile in TRANSFAC format
/taxon/List taxonomic groups
/collection/List collections (CORE, CNE, etc.)

Filter Parameters

  • tax_id — NCBI taxonomy ID (9606 for human)
  • collection — CORE, CNE, PHYLOFACTS, etc.
  • tf_class — TF structural class
  • name — TF name search
  • page, page_size — pagination

Example Calls

# Get CTCF binding profile
https://jaspar.elixir.no/api/v1/matrix/MA0139.1/

# Human CORE TF profiles
https://jaspar.elixir.no/api/v1/matrix/?tax_id=9606&collection=CORE&page_size=10

# Get profile in MEME format
https://jaspar.elixir.no/api/v1/matrix/MA0139.1/?format=meme

Response Format

JSON. Profiles include: matrix_id, name, pfm (position frequency matrix as A/C/G/T dict), sequence_logo URL, species, class, family.

API Docs

Swagger at https://jaspar.elixir.no/api/v1/docs/

Rate Limits

No published limits. Be reasonable.