This is documentation for Mathematica 8, which was
based on an earlier version of the Wolfram Language.

# SequenceAlignment

 SequenceAlignment finds an optimal alignment of sequences of elements in the strings or lists and , and yields a list of successive matching and differing sequences.
• SequenceAlignment 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, 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:
 GapPenalty 0 additional cost for each alignment gap IgnoreCase False whether to ignore case of letters in strings MergeDifferences True whether to combine adjacent differences Method "Global" alignment algorithm to be used SimilarityRules Automatic rules for similarities between elements
• SequenceAlignment attempts to find an alignment that maximizes the total similarity score.
• With the default setting SimilarityRules, 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.
Globally align two similar strings:
Global alignment of two strings:
Local alignment of the same strings:
Globally align two similar strings:
 Out[1]=

Global alignment of two strings:
 Out[1]=
Local alignment of the same strings:
 Out[2]=
 Options   (3)
Align two short protein sequences:
Assigning a negative score to the deletion of gives a different alignment:
By default, an alignment is found with two gaps:
Increasing the penalty for gaps forces another alignment with fewer gaps:
This gives insertions, deletions, and replacements as separate differences:
 Applications   (2)
This gives the global alignment of two similar strings:
This shows the difference between global and local string alignment:
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