jaspar-database
CommunityQuery TF binding profiles & scan DNA.
Education & Research#genomics#jaspar#transcription factors#motif analysis#dna binding#sequence scanning
Authorjaechang-hits
Version1.0.0
Installs0
System Documentation
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.
Dependency Matrix
Required Modules
requestspandasnumpymatplotlibpyJASPAR
Components
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: jaspar-database Download link: https://github.com/jaechang-hits/SciAgent-Skills/archive/main.zip#jaspar-database Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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