--> --- name: bio-clip-seq-clip-motif-analysis description: Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein. tool_type: cli primary_tool: HOMER measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---
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# COPYRIGHT NOTICE
# This file is part of the "Universal Biomedical Skills" project.
# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
# All Rights Reserved.
#
# This code is proprietary and confidential.
# Unauthorized copying of this file, via any medium is strictly prohibited.
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---
name: bio-clip-seq-clip-motif-analysis
description: Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.
tool_type: cli
primary_tool: HOMER
measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
allowed-tools:
- read_file
- run_shell_command
---
# CLIP Motif Analysis
## HOMER De Novo Motifs
```bash
# Extract sequences from peaks
bedtools getfasta -fi genome.fa -bed peaks.bed -fo peaks.fa
# Find enriched motifs
findMotifs.pl peaks.fa fasta output_dir \
-len 6,7,8 \
-rna
```
## MEME-ChIP
```bash
meme-chip -oc output_dir \
-dna \
peaks.fa
```
## Known Motif Enrichment
```bash
# HOMER known motif scan
findMotifs.pl peaks.fa fasta output_dir \
-rna \
-known
```
## Related Skills
- clip-peak-calling - Get peaks
- chip-seq/motif-analysis - General motif concepts
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
