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jaspar-database

Query transcription factor binding profiles from the JASPAR REST API.

1|Updated Mar 11, 2026
Search Tags:#bioinformatics#genomics#tf-binding#pwm#jaspar#pfm#motifs
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill jaspar-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: jaspar-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/jaspar-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill jaspar-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

JASPAR provides open-access transcription factor binding profiles; this skill enables programmatic access to TF binding profiles for motif analysis, regulatory interpretation, and comparative genomics.

Core Features & Use Cases

  • REST API access: query matrices, fetch full matrix details, and retrieve PFMs/PWMs.
  • PWM conversion & usage: convert PFMs to PWMs and score sequences for motif hits.
  • Use Case: identify candidate TF motifs in promoter regions or scanning regulatory elements across species.

Quick Start

Fetch the CTCF matrix MA0139.1 and convert it to PWM for sequence scanning.

Frequently Asked Questions about jaspar-database

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

FAQPage Schema
How do I fetch transcription factor binding profiles from the JASPAR database?▼

To fetch transcription factor binding profiles from the JASPAR database, you can query the JASPAR REST API to retrieve specific matrices and full matrix details for regulatory analysis.

Can I convert a PFM to a PWM for sequence scanning?▼

Yes, you can convert a PFM to a PWM. The skill handles PFM to PWM conversion and scores your sequences to identify motif hits for regulatory elements.

How do I scan promoter regions for TF binding motifs?▼

Scanning promoter regions for TF binding motifs involves fetching a specific TF matrix via the REST API, converting it to a PWM, and scanning your sequences for motif hits.

What is the best way to compare TF motifs across species using JASPAR profiles?▼

Comparing TF motifs across species uses JASPAR profiles by fetching matrix details for different species, converting PFMs to PWMs, and scanning sequences to discover regulatory elements.

Does this tool work for interpreting regulatory variants in genomics?▼

Yes, it works for interpreting regulatory variants by scanning sequences with TF binding PWMs to identify motif hits that may alter regulatory element function.

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