Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.
Reference examples tested with: bedtools 2.31+
Before using code patterns, verify installed versions match. If versions differ:
<tool> --version then <tool> --help to confirm flagsIf code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
"Find sequence motifs at my RBP binding sites" → Discover enriched RNA sequence motifs at CLIP-seq peaks to determine the binding specificity of an RNA-binding protein.
findMotifs.pl peaks.fa fasta output/ -rna (HOMER)bedtools getfasta to extract peak sequences firstGoal: Discover enriched RNA sequence motifs at CLIP-seq binding sites.
Approach: Extract FASTA sequences from peak regions using bedtools getfasta, then run HOMER findMotifs.pl in RNA mode to identify overrepresented 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 -oc output_dir \
-dna \
peaks.fa
# HOMER known motif scan
findMotifs.pl peaks.fa fasta output_dir \
-rna \
-known