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Mathematica > Core Language > String Manipulation > Sequence Alignment & Comparison > SequenceAlignment >

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.

MORE INFORMATION

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->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.

Basic Examples (2)

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]=

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:

LongestCommonSequence LongestCommonSubsequence SmithWatermanSimilarity NeedlemanWunschSimilarity SparseArray StringCases StringCount StringPosition BitXor

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