alterlab-jaspar
JASPAR Database
Overview
JASPAR (https://jaspar.elixir.no/) is the gold-standard open-access database of curated, non-redundant transcription factor (TF) binding profiles stored as position frequency matrices (PFMs). The current release, JASPAR 2026, added 265 new CORE profiles and promoted 41 from UNVALIDATED, for 2,633 latest-version CORE profiles across six taxonomic groups (the count the live API returns). Each profile is experimentally derived (ChIP-seq, SELEX, HT-SELEX, protein binding microarray, etc.) and curated. JASPAR 2026 also launched a Deep Learning (DL) collection — 1,259 BPNet models trained on ENCODE ChIP-seq for 240 human TFs — which is browsed and downloaded on the website and is not exposed through /api/v1/matrix/.
Key resources:
- JASPAR portal: https://jaspar.elixir.no/
- REST API: https://jaspar.elixir.no/api/v1/
- API docs: https://jaspar.elixir.no/api/v1/docs/
- Python access: direct REST (see
scripts/query_jaspar.py) or Biopython'sBio.motifs.jasparmodule (there is no standalonejasparPyPI package)
Scripts
scripts/query_jaspar.py — query the JASPAR REST API (stdlib only, JSON to stdout):