Increasingly complex (accurate) searches

Exact (StringSearch) CGCG

Regular expression (PrositeSearch) CGN{0-9}CG = CGAACG

Substitution matrix (BlastN) CGCG ~= CACG

Profile matrix (PSI-blast) CGc(g/a) ~ = CACG

Gaps (Gap-Blast) CGCG ~= CGAACG

Dynamic Programming (NW, SM) CGCG ~= CAGACG

WU

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