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JASPAR is an open-access database of manually curated, non-redundant transcription factor (TF) binding profiles, stored as position frequency matrices and used to predict where a TF may bind DNA. Anyone working with promoters, enhancers or regulatory variants can search it on the web, query it through a REST API, or load it in R or Python. This page maps the collections and access routes so you can pick the right one and cite it correctly. Information checked 2026-11-07.
Short answer
JASPAR holds binding profiles for transcription factors across six taxonomic groups. The current web release is the 11th (2026), distributed under a CC BY 4.0 licence. Each profile summarises observed TF-DNA interactions, and a profile can be converted into a scoring matrix to scan a sequence for likely binding sites.
Definition and scope
According to the JASPAR about page, the database is an open-access collection of manually curated, non-redundant TF binding profiles, represented as position frequency matrices (PFMs), together with deep learning models of TF binding. The profiles cover six taxonomic groups. The 2022 database paper (the 9th release) describes a PFM as a summary of the occurrences of each nucleotide at each position in a set of observed TF-DNA interactions.
JASPAR is a reference resource, not a motif-discovery program. It stores profiles that other work has derived and curated; it does not infer new motifs from your own sequencing data. For motifs in the protein sense, see the separate guide on protein motifs.
How JASPAR is used in practice
From PFM to PWM: the JASPAR scan idea
The 2022 paper explains that PFMs can be converted to position weight matrices (PWMs). A PWM scores each position of a candidate sequence, and positions scoring above a chosen threshold are predicted binding sites. This is the logic behind searching a sequence with a JASPAR motif. The JASPAR about page does not list a single tool named “Scan”; it lists several tools, including search by pattern, TFBS extraction, matrix clusters and enrichment analysis.
Genome-wide predictions and tracks
The 2022 paper reports genome-wide TFBS predictions generated by scanning genomes with CORE PFMs, for eight organisms. According to the JASPAR genome tracks page, the human JASPAR TFBS data appears as a native track in the UCSC Genome Browser, while tracks for other organisms are available through UCSC public hubs. That page also documents the TFBS tracks for UCSC and Ensembl (jaspar.elixir.no/genome-tracks).
Programmatic access
The JASPAR API page describes a RESTful API on the latest release, with endpoints for matrices, collections, the deep learning collection, taxa, species, TFFMs and JASPAR releases. Output formats include json, jsonp, jaspar, meme, transfac, pfm, yaml and bed. The matrices entry point is /api/v1/matrix. The 2022 paper also lists an R/Bioconductor package and a Python package, pyJASPAR, as access routes.
Collections and access routes
The table below is a cross-walk assembled from the JASPAR about page, API page and 2022 paper. It is meant to answer one question: which part of JASPAR should I use for my task?
| Component | What the source says it is | Source |
|---|---|---|
| CORE collection | Curated, non-redundant profiles from experimentally defined binding sites | About page |
| UNVALIDATED collection | Profiles without orthogonal literature support; to be used with caution | About page |
| Deep Learning collection | Interpretable deep learning models of TF binding, plus matrices derived from interpreting them | About page |
| TFFMs | Hidden-Markov models that capture dinucleotide dependencies, initialised from CORE PFMs | 2022 paper |
| Familial profiles | Profiles produced by hierarchical clustering of matrices | 2022 paper |
| Website | Search and browse; tools include Genome Tracks, TFBS extraction, search by pattern, matrix clusters and enrichment analysis | About page |
| REST API | Programmatic retrieval in json, meme, transfac, pfm, bed and other formats | API page |
| R/Bioconductor and pyJASPAR | Package access from R and Python | 2022 paper |
Where it matters for labs
- Cite the release. The API page asks users to cite the API and the specific release used. Because the database changes between releases, a methods section that names only “JASPAR” cannot be reproduced. Record the release, collection and matrix IDs you used; this follows the same logic as the FAIR data principles and a persistent identifier for each resource.
- Reuse terms. The about page gives the licence as CC BY 4.0, an attribution licence; see Creative Commons.
- Treat counts as release-specific. The 2022 paper reports 1,955 CORE PFMs: 841 vertebrate, 656 plant, 179 fungal, 150 insect, 43 nematode and 86 urochordate. Those figures describe the 9th release only.
- Pair with sequence work. Binding-site scans are often followed by primer design or alignment; see the guides on NCBI BLAST for primers and EMBOSS Needle, or on choosing a genome assembler.
Common misunderstandings
- JASPAR is not a motif finder. It supplies curated profiles; discovery from your own data needs other software.
- A profile is not proof of binding. A PWM score above threshold is a prediction. The UNVALIDATED collection in particular lacks orthogonal literature support.
- 2022 figures are not current. The paper describes the 9th release; the website now serves the 11th (2026).
- The name is not a general word. The searches “JASPAR name” and “Jaspar software” usually refer to this database, which is hosted by ELIXIR Norway.
FAQ
What is a JASPAR motif?
A JASPAR motif is a TF binding profile stored as a PFM, a table of nucleotide counts at each position of observed binding sites. It can be shown as a sequence logo or converted to a PWM for scoring.
How do I use JASPAR?
Search the website for a TF or species, download the matrix, or retrieve it from the API in a format such as meme or transfac. You can also use the R/Bioconductor or pyJASPAR packages. Always note the release.
What is JASPAR 2022, and what about 2024 and 2026?
JASPAR 2022 is the 9th release, described in a published paper. The website currently serves the 11th release (2026). This page does not give figures for releases other than 2022.
Is JASPAR a database or software?
It is a database with accompanying tools: a web interface, an API, genome tracks, enrichment analysis and other utilities listed on its about page.
Sources
- JASPAR, About, jaspar.elixir.no/about (read 2026-11-07).
- JASPAR, API documentation, jaspar.elixir.no/api (read 2026-11-07).
- JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles, PMC8728201 (read 2026-11-07).
