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jaspar-database

Query the JASPAR CORE database for transcription factor binding motifs and return PFMs/PWMs.

48|6|Updated Mar 9, 2026
Search Tags:#bioinformatics#genomics#jaspar#tfbs#motifs#pwms#sequence-scanning
One-click install
npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill jaspar-database-qinyan-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: jaspar-database
Source: https://github.com/qinyan-ai/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/jaspar-database
Command: npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill jaspar-database-qinyan-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Access to open, curated transcription factor binding profiles and practical tools to apply them for motif discovery, regulatory interpretation, and genomic analyses.

Core Features & Use Cases

  • Search and fetch matrices from the JASPAR CORE collection by name, species, and class to obtain PFMs/PWMs.
  • Scan DNA sequences for TF binding motifs using PFMs/PWMs and compute motif scores for hit identification.
  • Variant interpretation assess how SNPs or mutations may alter TF binding by comparing ref and alt sequences across strands.
  • Use case: evaluate regulatory variants in GWAS loci by scanning promoter/enhancer regions for disrupted motifs and potential target TFs.

Quick Start

Scan a promoter sequence for TF binding motifs using a CORE collection matrix MA0139.1 and report the hits.

Frequently Asked Questions about jaspar-database

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

FAQPage Schema
How do I retrieve transcription factor binding motifs from the JASPAR CORE database?▼

To retrieve transcription factor binding motifs, search the JASPAR CORE collection by name, species, or class to obtain position frequency matrices and position weight matrices for downstream sequence analysis.

Can I scan DNA sequences for TF binding sites using PWMs?▼

Yes, you can scan DNA sequences for TF binding sites by applying position weight matrices to compute motif scores and identify specific hit locations across both strands of the input sequence.

How do SNPs or mutations alter transcription factor binding?▼

Variant interpretation assesses how SNPs alter transcription factor binding by comparing reference and alternate sequences across both strands, evaluating changes in PWM scores to determine disrupted motifs.

Does this skill support regulatory variant interpretation in GWAS loci?▼

Yes, regulatory variant interpretation in GWAS loci is supported by scanning promoter and enhancer regions with JASPAR matrices to identify disrupted motifs and potential target transcription factors.

What is the best way to analyze promoter and enhancer regions for TF binding sites across diverse species?▼

The best way to analyze promoter and enhancer regions is querying the JASPAR CORE collection across diverse species and TF classes, fetching PFMs and PWMs for sequence scanning and matrix manipulation.

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