jaspar-database

Query JASPAR transcription factor binding profiles and scan DNA sequences via REST API.

Updated Mar 10, 2026

Search Tags:#genomics #pwm #jaspar #transcription factors #motif analysis #binding sites

Ready to run

npx skills add https://github.com/felixboehm/biochem-allergy --skill jaspar-database-felixboehm

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: jaspar-database
Source: https://github.com/felixboehm/biochem-allergy/tree/main/.claude/skills/jaspar-database
Command: npx skills add https://github.com/felixboehm/biochem-allergy --skill jaspar-database-felixboehm

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides programmatic access to the JASPAR database, enabling researchers to find and analyze transcription factor binding sites (TFBS) within DNA sequences.

Core Features & Use Cases

Search TF Profiles: Find binding profiles by TF name, species, or class.
Scan DNA Sequences: Predict potential TF binding sites in a given DNA sequence.
Variant Impact Analysis: Assess how genetic variants might affect TF binding.
Use Case: Determine if a specific genetic variant identified in a GWAS study disrupts the binding site of a known transcription factor, potentially explaining its functional impact.

Quick Start

Search JASPAR for transcription factor binding profiles for CTCF in humans.

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, this Skill queries JASPAR profiles via the REST API and predicts potential motif matches. It retrieves position weight matrices for specified transcription factors and evaluates your sequence against them.

Can I analyze genetic variant impact on transcription factor binding affinity with JASPAR?▼

Yes, you can assess genetic variant impact on transcription factor binding affinity by comparing reference and alternate allele scores against JASPAR position weight matrices. This evaluates whether variants disrupt predicted motif matches.

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

You can search for transcription factor binding profiles by filtering JASPAR database records using TF name, species, or class. The Skill sends targeted queries to the JASPAR REST API and returns matching position weight matrix profiles.

Does this JASPAR Skill require Python packages like numpy and requests to query motifs?▼

Yes, querying JASPAR motifs requires the Python packages requests and numpy. Requests handles the JASPAR REST API calls for profile retrieval, while numpy processes the position weight matrices used in motif analysis.

What is the best way to programmatically retrieve position weight matrices for motif analysis?▼

The best way to programmatically retrieve position weight matrices for motif analysis is using the JASPAR REST API. This Skill automates data retrieval and sequence scanning directly in Python for regulatory genomics research.

Why use JASPAR position weight matrices instead of other motif analysis approaches for regulatory genomics?▼

JASPAR position weight matrices provide curated, open-access transcription factor binding profiles specifically designed for regulatory genomics. This approach directly integrates REST API retrieval with Python sequence scanning to identify predicted binding sites.