db-jaspar

Name: db-jaspar
Availability: InStock
Author: biomaps-infra

Query JASPAR for transcription factor binding site profiles and matrices.

Updated Mar 13, 2026

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

Ready to run

npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-jaspar

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: db-jaspar
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-jaspar
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-jaspar

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill helps researchers and bioinformaticians quickly access and utilize the JASPAR database to understand transcription factor binding sites, aiding in the interpretation of genomic regulatory elements and variants.

Core Features & Use Cases

Search TF Profiles: Find transcription factor binding profiles by name, species, or class.
Fetch Matrices: Retrieve specific Position Frequency Matrices (PFMs) or convert them to Position Weight Matrices (PWMs).
Scan DNA Sequences: Predict TF binding sites within a given DNA sequence.
Variant Impact Analysis: Assess how genetic variants might affect TF binding.
Use Case: Identify all potential binding sites for a specific transcription factor (e.g., CTCF) within a gene's promoter region to understand its regulatory role.

Quick Start

Use the db-jaspar skill to search for transcription factor profiles for the human species.

Frequently Asked Questions about db-jaspar

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?▼

To retrieve transcription factor binding profiles from the JASPAR database, you can search by TF name, species, or class to fetch specific Position Frequency Matrices (PFMs) and convert them to Position Weight Matrices (PWMs) for regulatory genomics analysis.

Can I scan a DNA sequence for transcription factor binding sites using PWMs?▼

Yes, you can scan a given DNA sequence for transcription factor binding sites using PWMs. This process predicts potential binding locations within your sequence to help interpret genomic regulatory elements.

How do I analyze the impact of genetic variants on transcription factor binding sites?▼

To analyze the impact of genetic variants on transcription factor binding sites, you can use this functionality to assess how sequence changes might affect TF binding affinity and disrupt regulatory elements within the genome.

What is the difference between a PFM and a PWM in motif analysis?▼

In motif analysis, a PFM (Position Frequency Matrix) represents the observed nucleotide counts at each position, while a PWM (Position Weight Matrix) converts these frequencies into log-odds scores to evaluate sequence binding affinity.

Do I need numpy installed to query JASPAR matrices for motif analysis?▼

Yes, you need numpy installed to query JASPAR matrices for motif analysis. The skill requires both the requests and numpy dependencies to fetch profiles from the database and perform the necessary numerical calculations.

Can I search for transcription factor profiles by species and class?▼

Yes, you can search for transcription factor profiles by species and class. This allows you to filter JASPAR database queries to find specific TF binding site profiles relevant to your target organism or protein classification.