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


Basic Examples  (2)

SmithWaterman similarity between two strings:

SmithWaterman similarity between two vectors:

Introduced in 2008