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SmithWatermanSimilarity

SmithWatermanSimilarity[u,v]

gives a number representing the Smith–Waterman similarity between strings, vectors or bio sequences u and v.

Details and Options

SmithWatermanSimilarity[u,v] finds an optimal local alignment between the elements of u and v, and returns the number of one-element matches.
For strings, setting the option IgnoreCase->True makes SmithWatermanSimilarity treat lowercase and uppercase letters as equivalent.
With the default setting SimilarityRules->Automatic, each match between two characters contributes 1 to the total similarity score, while each mismatch, insertion, or deletion contributes -1.
The option GapPenalty specifies an additional cost to be subtracted from the similarity score for any run of insertions or deletions.

Examples

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Basic Examples (3)

Smith–Waterman similarity between two strings:

Smith–Waterman similarity between two vectors:

Smith–Waterman similarity between two bio sequences:

Options (1)

SimilarityRules (1)

The "SimilarDegenerateBases" setting allows a higher similarity for matching degenerate terms in biomolecular sequences:

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