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

- 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:
-
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->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.
Examples
open allclose allBasic Examples (3)
Globally align two similar strings:
Global alignment of two strings:
Local alignment of the same strings:
Global alignment of two instances of BioSequence:
Options (4)
GapPenalty (1)
Applications (2)
Text
Wolfram Research (2008), SequenceAlignment, Wolfram Language function, https://reference.wolfram.com/language/ref/SequenceAlignment.html (updated 2020).
CMS
Wolfram Language. 2008. "SequenceAlignment." Wolfram Language & System Documentation Center. Wolfram Research. Last Modified 2020. https://reference.wolfram.com/language/ref/SequenceAlignment.html.
APA
Wolfram Language. (2008). SequenceAlignment. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/SequenceAlignment.html