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jaspar-database

Query the JASPAR API for transcription factor binding profiles and motif matrices.

Updated Sep 9, 2026
Search Tags:#bioinformatics#genomics#motif#pwm#transcription factor#jaspar#pfm
One-click install
npx skills add https://github.com/xlinh2301/EditCTC --skill jaspar-database-xlinh2301
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: jaspar-database
Source: https://github.com/xlinh2301/EditCTC/tree/main/.agents/skills/jaspar-database
Command: npx skills add https://github.com/xlinh2301/EditCTC --skill jaspar-database-xlinh2301

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires polite-http, and includes scripts (resource) components.

What problem does it solve? Retrieving transcription factor (TF) binding profiles from the JASPAR database requires resolving gene symbols to stable Matrix IDs, respecting API rate limits, and converting between matrix formats. This Skill wraps the JASPAR REST API in ready-to-run scripts so you can fetch Position Frequency Matrices (PFMs), compute Position Weight Matrices (PWMs), and pull TF metadata without writing API client code. ## Core Features & Use Cases - TF Name Resolution: Map gene symbols (e.g., JUN) to stable JASPAR Matrix IDs (e.g., MA0488.2) using taxonomy-filtered search. - Motif Retrieval & Conversion: Fetch PFMs in multiple formats (JSON, MEME, TRANSFAC, JASPAR, YAML) and compute log-odds PWMs with configurable pseudocounts. - Sequence-Based Inference: Infer candidate TF binding matrices directly from a raw protein sequence, plus retrieve TF Flexible Model (TFFM) metadata. - Use Case: Given a ChIP-seq peak region, resolve the candidate TF "CTCF" to its Matrix ID, download its PFM in MEME format, and feed it into a motif-scanning tool to locate binding sites. ## Quick Start Ask the assistant to resolve the transcription factor JUN in human (tax_id 9606) and retrieve its position frequency matrix from JASPAR.

Frequently Asked Questions about jaspar-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I get a transcription factor binding motif from JASPAR?▼

First resolve the gene symbol to a Matrix ID using resolve_tf_id with a taxonomy ID, then call get_tf_motif with that Matrix ID. The script returns the Position Frequency Matrix, with optional formats like MEME, TRANSFAC, or JASPAR.

How to convert a JASPAR PFM to a PWM position weight matrix?▼

Use the get_tf_pwm command with a Matrix ID, which fetches the PFM and converts it to log2-odds scores using a uniform 0.25 background. The --pseudocount flag adjusts smoothing, defaulting to 0.8 per base.

Why does get_tf_motif reject my gene symbol like JUN?▼

The motif, metadata, and PWM commands require a stable JASPAR Matrix ID in the format MA0488.2, not a gene symbol. Run resolve_tf_id with the gene name and a tax_id (9606 for human, 10090 for mouse) first to obtain the Matrix ID.

Can JASPAR predict tissue-specific transcription factor binding?▼

No. JASPAR stores potential binding profiles derived from experiments, not actual tissue-specific occupancy. Determining in-vivo binding requires epigenetic context such as ATAC-seq or ChIP-seq data from the relevant tissue.

What output formats does the JASPAR API support for motifs?▼

The get_tf_motif and get_tf_metadata commands support json (default), jsonp, jaspar, meme, transfac, pfm, and yaml via the --format flag. Non-JSON formats are fetched as raw text from the API.

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