bio-motif-search

npx skills add majiayu000/claude-skill-registry --skill motif-search-gptomics-bioskills-2 --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# Motif Search Find patterns and motifs in biological sequences using Biopython and regex. ## Required Imports ```python from Bio.Seq import Seq from Bio import motifs import re ``` ## Core Methods ### find() - First Occurrence ```python seq = Seq('ATGCGAATTCGATCGAATTCGATC') pos = seq.find('GAATTC') # Returns 4 (first position) ``` Returns -1 if not found. ### count() - Count Occurrences ```python seq = Seq('ATGCGAATTCGATCGAATTCGATC') n = seq.count('GAATTC') # Returns 2 ``` ### find() with Start Position ```python seq = Seq('ATGCGAATTCGATCGAATTCGATC') first = seq.find('GAATTC') # 4 second = seq.find('GAATTC', 5) # 14 (search from position 5) ``` ## Code Patterns ### Find All Occurrences ```python def find_all(seq, pattern): pattern = str(pattern) seq_str = str(seq) positions = [] pos = seq_str.find(pattern) while pos != -1: positions.append(pos) pos = seq_str.find(pattern, pos + 1) return positions seq = Seq('ATGCGAATTCGATCGAATTCGATC') positions = find_all(seq, 'GAATTC') # [4, 14] ``` ### Search Both Strands ```python def find_both_strands(seq, pattern): results = [] for pos in find_all(seq, pattern): results.append(('+', pos)) rc = seq.reverse_complement() for pos in find_all(rc,