Individual skill
bio-motif-search
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.
skills/bioskills/bio-sequence-manipulation-motif-search/SKILL.md
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SKILL.mdcore · 11,925 bytesSKILL.mdcore · 11,925 bytesSKILL.mdcore · 11,925 bytesSKILL.mdcore · 11,925 bytesSKILL.mdcore · 11,925 bytesSKILL.mdcore · 11,925 bytesSKILL.mdcore · 11,925 bytesSKILL.mdcore · 11,925 bytesreferences/usage-guide.mddoc · 3,561 bytesscripts/basic_search.pyruns · 1,388 bytesscripts/motif_files.pyruns · 1,937 bytesscripts/pwm_search.pyruns · 2,204 bytesscripts/regex_search.pyruns · 1,575 bytes
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## Version Compatibility
Reference examples tested with: BioPython 1.83+
Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
# Motif Search
**"Search for a sequence motif or binding-site pattern"** -> Scan sequences for a fixed motif, a degenerate IUPAC consensus, or a probabilistic PWM, on one or both strands, and locate transcription-factor binding sites, regulatory elements, or custom patterns.
- Python: `Bio.SeqUtils.nt_search` (IUPAC + overlaps), `re` (regex/lookahead), `Bio.motifs` (PWM/PSSM scoring + matrix file parsing)