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jaspar-database

Retrieve TF binding profiles from JASPAR 2024 and scan DNA sequences for TFBS.

298|27|Updated Feb 18, 2026
Search Tags:#genomics#jaspar#transcription factors#motif analysis#dna binding#sequence scanning
One-click install
npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill jaspar-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: jaspar-database
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/genomics-bioinformatics/jaspar-database
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill jaspar-database

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, numpy, matplotlib, pyJASPAR, 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 retrieve transcription factor binding profiles (PFMs/PWMs) and scan DNA sequences for binding sites, streamlining regulatory sequence analysis.

Core Features & Use Cases

  • Profile Retrieval: Fetch Position Frequency Matrices (PFMs) and Position Weight Matrices (PWMs) for specific transcription factors (TFs) by name, ID, species, or TF family.
  • Sequence Scanning: Scan DNA sequences for predicted TF binding sites (TFBS) using downloaded PWMs.
  • Data Export: Generate motif libraries in standard formats like MEME for downstream analysis.
  • Use Case: Identify all binding sites for the CTCF transcription factor within a given promoter region by downloading its PWM from JASPAR and scanning the sequence.

Quick Start

Use the jaspar-database skill to find all JASPAR CORE profiles for Homo sapiens.

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 profiles from the JASPAR database?▼

Retrieve transcription factor binding profiles by querying the JASPAR 2024 database via REST API and pyJASPAR. You can fetch Position Frequency Matrices (PFMs) and Position Weight Matrices (PWMs) for specific TFs by name, ID, species, or TF family.

How do I scan DNA sequences for transcription factor binding sites?▼

Scan DNA sequences for predicted transcription factor binding sites (TFBS) using downloaded PWMs. The Skill accesses JASPAR PWMs to scan your regulatory sequences and identify potential TF binding site locations.

Can I export JASPAR motif libraries in MEME format for downstream analysis?▼

Yes, you can export motif libraries in standard MEME format. This enables seamless downstream motif enrichment analysis and integration with sequence analysis pipelines.

Does this Skill support querying JASPAR profiles for specific species like Homo sapiens?▼

Yes, the Skill supports querying JASPAR CORE profiles for specific species such as Homo sapiens. You can filter transcription factor binding profiles by species, TF family, or specific TF name.

What Python libraries do I need to analyze transcription factor binding motifs?▼

You need requests, pandas, numpy, matplotlib, and pyJASPAR. These dependencies support REST API access, matrix data manipulation, visualization, and direct queries to the JASPAR database.

How do I identify CTCF binding sites within a promoter region?▼

Identify CTCF binding sites by downloading its PWM from the JASPAR database and scanning your target promoter sequence. The Skill streamlines this regulatory sequence analysis workflow.

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