jaspar-database
Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs). Search by TF name, species, or class; scan DNA sequences for TF binding sites; compare matrices; essential for regulatory genomics, motif analysis, and GWAS regulatory variant interpretation.
npx skills add LeonChaoX/qinyan-academic-skills --skill jaspar-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# JASPAR Database ## Overview JASPAR (https://jaspar.elixir.no/) is the gold-standard open-access database of curated, non-redundant transcription factor (TF) binding profiles stored as position frequency matrices (PFMs). JASPAR 2024 contains 1,210 non-redundant TF binding profiles for 164 eukaryotic species. Each profile is experimentally derived (ChIP-seq, SELEX, HT-SELEX, protein binding microarray, etc.) and rigorously validated. **Key resources:** - JASPAR portal: https://jaspar.elixir.no/ - REST API: https://jaspar.elixir.no/api/v1/ - API docs: https://jaspar.elixir.no/api/v1/docs/ - Python package: `jaspar` (via Biopython) or direct API ## When to Use This Skill Use JASPAR when: - **TF binding site prediction**: Scan a DNA sequence for potential binding sites of a TF - **Regulatory variant interpretation**: Does a GWAS/eQTL variant disrupt a TF binding motif? - **Promoter/enhancer analysis**: What TFs are predicted to bind to a regulatory element? - **Gene regulatory network construction**: Link TFs to their target genes via motif scanning - **TF family analysis**: Compare binding profiles across a TF family (e.g., all homeobox factors) - **ChIP-seq analysis**: Find known TF
- Overview
- When to Use This Skill
- Core Capabilities
- 1. JASPAR REST API
- 2. Search for TF Profiles
- 3. Fetch a Specific Matrix (PFM/PWM)
- 4. Download PFM/PWM as Matrix
- 5. Scan a DNA Sequence for TF Binding Sites
- 6. Scan Both Strands
- 7. Variant Impact on TF Binding
- Query Workflows
- Workflow 1: Find All TF Binding Sites in a Promoter
- Workflow 2: SNP Impact on TF Binding (Regulatory Variant Analysis)
- Workflow 3: Motif Enrichment Analysis
What does the jaspar-database skill do?
Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs). Search by TF name, species, or class; scan DNA sequences for TF binding sites; compare matrices; essential for regulatory genomics, motif analysis, and GWAS regulatory variant interpretation.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill jaspar-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.