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BI
bio-chipseq-motif-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-chipseq-motif-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: findMotifsGenome.pl peaks.bed hg38 output/ (HOMER), meme-chip -db JASPAR peaks.fa (MEME).
- Find enriched motifs in my ChIP-seq peaks" → Discover de novo DNA-binding motifs and test for known TF motif enrichment in peak sequences. CLI: findMotifsGenome.pl peaks.bed hg38 output/ (HOMER), meme-chip -db JASPAR peaks.fa (MEME).
- Identify DNA sequence motifs enriched in ChIP-seq or ATAC-seq peaks to discover transcription factor binding sites.
- perl /path/to/homer/configureHomer.pl -install hg38 perl /path/to/homer/configureHomer.pl -install mm10.
Source Doc
Excerpt From SKILL.md
Tool Comparison
| Tool | Strengths | Use Case |
|---|---|---|
| HOMER | Fast, comprehensive, built-in databases | General motif analysis |
| MEME-ChIP | Multiple algorithms, web interface | Publication-quality |
| MEME | De novo discovery only | Simple discovery |
| FIMO | Known motif scanning | Genome-wide scanning |
Installation
conda install -c bioconda homer
## De Novo Motif Discovery
**Goal:** Discover enriched DNA-binding motifs directly from ChIP-seq peak sequences.
**Approach:** Run findMotifsGenome.pl on a peak BED file with a specified fragment size, optionally providing background regions and target motif lengths.
```bash
Use cases
- Use when finding enriched DNA motifs in peak sequences.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- peak-calling - Generate input peaks
- peak-annotation - Annotate peaks with genes
- atac-seq/footprinting - TF footprint analysis
- genome-intervals - BED file operations
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