SequenceAlignment

SequenceAlignment[s1, s2]
finds an optimal alignment of sequences of elements in the strings or lists and , and yields a list of successive matching and differing sequences.

Details and OptionsDetails and Options

  • SequenceAlignment[s1, s2] gives a list of the form where each is either a single string or sequence of list elements u, representing a matching segment, or a pair , representing segments that differ between the .
  • SequenceAlignment by default finds a global Needleman-Wunsch alignment of the complete strings or lists and .
  • With the option setting Method->"Local", it finds a local Smith-Waterman alignment.
  • For sufficiently similar strings or lists, local and global alignment methods give the same result.
  • The following options can be given:
  • GapPenalty0additional cost for each alignment gap
    IgnoreCaseFalsewhether to ignore case of letters in strings
    MergeDifferencesTruewhether to combine adjacent differences
    Method"Global"alignment algorithm to be used
    SimilarityRulesAutomaticrules for similarities between elements
  • SequenceAlignment attempts to find an alignment that maximizes the total similarity score.
  • With the default setting SimilarityRules->Automatic, each match between two elements contributes 1 to the total similarity score, while each mismatch, insertion, or deletion contributes -1.
  • Various named similarity matrices are supported, as specified in the notes for SimilarityRules.

ExamplesExamplesopen allclose all

Basic Examples (2)Basic Examples (2)

Globally align two similar strings:

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Global alignment of two strings:

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Local alignment of the same strings:

In[2]:=
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