gives a number representing the SmithWaterman similarity between strings or vectors u and v.

Details and OptionsDetails 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.

ExamplesExamplesopen allclose all

Basic Examples  (2)Basic Examples  (2)

SmithWaterman similarity between two strings:

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SmithWaterman similarity between two vectors:

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Introduced in 2008