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motif-search

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Find sequence motifs, degenerate IUPAC patterns, and transcription-factor binding sites in DNA/RNA using Biopython and regex, including position weight matrix (PWM/PSSM) scoring. Use when locating regulatory elements, counting overlapping motif occurrences, scanning for binding-site matches above a significance threshold, or reading motif matrices from JASPAR/MEME/TRANSFAC files. For restriction enzyme sites, use restriction-analysis/restriction-sites.

When to use

• locating regulatory elements
• counting overlapping motif occurrences
• scanning for binding-site matches above a significance threshold
• reading motif matrices from JASPAR/MEME/TRANSFAC files
• scanning for fixed motifs
• scanning for degenerate IUPAC consensus
• scanning for probabilistic PWM
• locating transcription-factor binding sites

When not to use

• restriction enzyme sites

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