jaspar-database

Query JASPAR transcription factor profiles and scan DNA sequences for binding sites.

1|Updated Mar 4, 2026

Search Tags:#genomics #pwm #jaspar #tfbs #pfm #motifs #sequence-scanning

Ready to run

npx skills add https://github.com/Hung-3008/agusta --skill jaspar-database-hung-3008

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: jaspar-database
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/jaspar-database
Command: npx skills add https://github.com/Hung-3008/agusta --skill jaspar-database-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Querying and interpreting transcription factor binding profiles can be time-consuming and error-prone. This skill centralizes access to JASPAR profiles, enabling fast searches, matrix retrieval, sequence scanning, and motif-based analyses for regulatory genomics tasks.

Core Features & Use Cases

Search by TF name, species, or class to retrieve PFMs/PWMs from the CORE and other collections.
Fetch PFMs, convert to PWMs, and scan DNA sequences for potential binding sites with scores.
Compare matrices and apply motifs to regulatory variant interpretation, promoter/enhancer analysis, and gene regulatory network construction.
Example: identify potential binding motifs across a promoter region for a given TF and species.

Quick Start

Provide a DNA sequence and a TF name to retrieve JASPAR matrices and identify potential binding sites.

Frequently Asked Questions about jaspar-database

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

FAQPage Schema

How do I scan a DNA sequence for transcription factor binding sites using JASPAR profiles?▼

To scan DNA sequences for transcription factor binding sites, you provide a DNA sequence and a TF name to retrieve JASPAR PFMs and PWMs, then scan for potential binding sites with scores returned in JSON format. This requires internet access to the JASPAR REST API.

Can I retrieve position frequency matrices from the JASPAR CORE collection by species or TF class?▼

Yes, you can retrieve position frequency matrices from the JASPAR CORE and other collections by searching specifically for transcription factors using TF name, species, or class. Matrix details are returned in JSON format for downstream regulatory genomics workflows.

What is the best way to convert JASPAR PFMs to PWMs for sequence scanning?▼

The best way to convert JASPAR PFMs to PWMs for sequence scanning is to fetch the PFM from the JASPAR REST API and apply the built-in matrix conversion and scanning logic. This returns potential binding sites with scores for your DNA sequences.

Does this approach support regulatory variant interpretation and gene regulatory network construction?▼

Yes, this approach supports regulatory variant interpretation, promoter and enhancer analysis, and gene regulatory network construction. You apply retrieved JASPAR motifs and matrix comparisons directly to these genomics workflows to identify functional regulatory elements.

Do I need internet access to query JASPAR transcription factor binding profiles?▼

Yes, you need internet access to query JASPAR transcription factor binding profiles because the skill communicates directly with the JASPAR REST API to fetch PFMs, PWMs, and scan sequences. Without connectivity, matrix retrieval and sequence scanning cannot execute.

What limitations exist when comparing matrices for motif-based genomics analysis?▼

A key limitation is that matrix comparisons and sequence scanning depend entirely on the availability and coverage of profiles within the JASPAR collections you query. Results are constrained by the CORE and other specified collections accessed via the REST API.