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jaspar.md
50 lines · skills/database-lookup/references/jaspar.md at 5f2bc03
JASPAR (Transcription Factor Binding Profiles)
Raw lines 1 to 211## Key Endpoints
13| Endpoint | Description |
14|----------|-------------|
15| `/matrix/` | List all TF binding profiles |
16| `/matrix/{matrix_id}/` | Specific profile (e.g. MA0139.1 for CTCF) |
17| `/matrix/?tax_id={id}&collection=CORE` | Filter by species + collection |
18| `/matrix/{id}/?format=jaspar` | Profile in JASPAR format |
19| `/matrix/{id}/?format=meme` | Profile in MEME format |
20| `/matrix/{id}/?format=transfac` | Profile in TRANSFAC format |
21| `/taxon/` | List taxonomic groups |
22| `/collections/` | List collections (CORE, CNE, etc.) |
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 |
/collections/ | List collections (CORE, CNE, etc.) |
24## Filter Parameters
25- `tax_id` — NCBI taxonomy ID (9606 for human)
26- `collection` — CORE, CNE, PHYLOFACTS, etc.
27- `tf_class` — TF structural class
28- `name` — TF name search
29- `page`, `page_size` — pagination
Filter Parameters
tax_id— NCBI taxonomy ID (9606 for human)collection— CORE, CNE, PHYLOFACTS, etc.tf_class— TF structural classname— TF name searchpage,page_size— pagination
31## Example Calls
32```
33# Get CTCF binding profile
34https://jaspar.elixir.no/api/v1/matrix/MA0139.1/
36# Human CORE TF profiles
37https://jaspar.elixir.no/api/v1/matrix/?tax_id=9606&collection=CORE&page_size=10
39# Get profile in MEME format
40https://jaspar.elixir.no/api/v1/matrix/MA0139.1/?format=meme
41```
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=meme43## Response Format
44JSON. Profiles include: `matrix_id`, `name`, `pfm` (position frequency matrix as A/C/G/T dict), `sequence_logo` URL, `species`, `class`, `family`.
Response Format
JSON. Profiles include: matrix_id, name, pfm (position frequency matrix as A/C/G/T dict), sequence_logo URL, species, class, family.