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jaspar-database

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

Updated Mar 15, 2026
Search Tags:#genomics#pwm#jaspar#transcription factors#motif analysis#binding sites
One-click install
npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill jaspar-database-sagunkayastha
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: jaspar-database
Source: https://github.com/sagunkayastha/claude_skills_collection/tree/main/scientific-databases/jaspar-database
Command: npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill jaspar-database-sagunkayastha

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, numpy, and includes references (resource) components.

What problem does it solve?

This Skill provides programmatic access to the JASPAR database, enabling users to find and analyze transcription factor binding site profiles (PWMs/PFMs) for regulatory genomics research.

Core Features & Use Cases

  • Search TF Profiles: Find binding profiles by TF name, species, or class.
  • Fetch Specific Matrices: Retrieve detailed PFM/PWM data for a given matrix ID.
  • Scan DNA Sequences: Predict TF binding sites within a given DNA sequence.
  • Variant Impact Analysis: Assess how SNPs might affect TF binding.
  • Use Case: Identify all potential binding sites for CTCF in a human promoter region to understand gene regulation.

Quick Start

Search JASPAR for human transcription factor binding profiles related to 'CTCF'.

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 site profiles from JASPAR?▼

Scan DNA sequences for motif occurrences by using the JASPAR REST API to fetch PWMs and predict transcription factor binding sites within your input sequence programmatically.

Can I assess how SNPs affect TF binding using JASPAR?▼

Perform variant impact analysis by fetching transcription factor binding profiles from JASPAR to assess how SNPs might affect TF binding sites in regulatory genomics workflows.

What is the best way to find human CTCF binding profiles for motif analysis?▼

Search the JASPAR database by transcription factor name and species to retrieve human CTCF binding profiles, returning position frequency matrices for regulatory genomics analysis.

Does this JASPAR query tool require numpy and requests to run?▼

Yes, accessing JASPAR transcription factor binding profiles requires the requests library for REST API data retrieval and numpy for numerical processing of PWM matrices.

How do I search JASPAR for transcription factor profiles by class or species?▼

Query the JASPAR REST API by transcription factor name, species, or class to retrieve matching position frequency matrices and position weight matrices for motif analysis.

Can I use JASPAR PWMs to interpret GWAS variants in regulatory regions?▼

Use JASPAR position weight matrices to interpret GWAS variants by scanning DNA sequences to predict transcription factor binding sites and assess variant impacts on binding affinity.

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