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
# 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
meme-chip -oc output_dir \
-dna \
peaks.fa
Known Motif Enrichment
# 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
1---2name: bio-clip-seq-clip-motif-analysis3description: <!--4---5<!--6# COPYRIGHT NOTICE7# This file is part of the "Universal Biomedical Skills" project.8# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>9# All Rights Reserved.10#11# This code is proprietary and confidential.12# Unauthorized copying of this file, via any medium is strictly prohibited.13#14# Provenance: Authenticated by MD BABU MIA1516-->1718---19name: bio-clip-seq-clip-motif-analysis20description: Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.21tool_type: cli22primary_tool: HOMER23measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.24allowed-tools:25 - read_file26 - run_shell_command27---2829# CLIP Motif Analysis3031## HOMER De Novo Motifs3233```bash34# Extract sequences from peaks35bedtools getfasta -fi genome.fa -bed peaks.bed -fo peaks.fa3637# Find enriched motifs38findMotifs.pl peaks.fa fasta output_dir \39 -len 6,7,8 \40 -rna41```4243## MEME-ChIP4445```bash46meme-chip -oc output_dir \47 -dna \48 peaks.fa49```5051## Known Motif Enrichment5253```bash54# HOMER known motif scan55findMotifs.pl peaks.fa fasta output_dir \56 -rna \57 -known58```5960## Related Skills6162- clip-peak-calling - Get peaks63- chip-seq/motif-analysis - General motif concepts646566<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->
Run npx skillmds@latest add freedomintelligence/bio-clip-seq-clip-motif-analysis in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.
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FreedomIntelligence (@freedomintelligence) published this skill. Their other Agent Skills are listed on their SkillMD profile.