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SequenceAlignment

SequenceAlignment[s1, s2]
finds an optimal alignment of sequences of elements in the strings or lists s1 and s2, and yields a list of successive matching and differing sequences.
  • SequenceAlignment[s1, s2] gives a list of the form {seg1, seg2, ...} where each segi is either a single string or sequence of list elements u, representing a matching segment, or a pair {u1, u2}, representing segments that differ between the si.
  • SequenceAlignment by default finds a global Needleman-Wunsch alignment of the complete strings or lists s1 and s2.
  • 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 which 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.
EXAMPLESCLOSE ALL
Basic Examples   (2)
Globally align two similar strings:
Global alignment of two strings:
Local alignment of the same strings:
Globally align two similar strings:
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Global alignment of two strings:
In[1]:=
Click for copyable input
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Local alignment of the same strings:
In[2]:=
Click for copyable input
Out[2]=
Options   (3)
Align two short protein sequences:
Assigning a negative score to the deletion of "V" 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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