drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/jaspar.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
JASPAR (Transcription Factor Binding Profiles)		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/jaspar.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

JASPAR (Transcription Factor Binding Profiles)

Base URL

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

Auth

No auth required.

Key Endpoints

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	Profile 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.