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BUILT-IN MATHEMATICA SYMBOL
SimilarityRules
SimilarityRules
is an option for functions such as SequenceAlignment that gives a list of rules for similarity scores to assume between pairs of elements.
Details
- The setting for SimilarityRules must consist of a list of rules of the form
, where the 
give elements to compare, and v gives their similarity. - The
can be either explicit characters or other elements, or patterns. - A rule for
gives the score for a deletion; a rule for 
gives the score for an insertion. - SimilarityRules->Automatic is effectively equivalent to
, giving a score of 
for any pair of identical elements, and a score of 
for any mismatch, deletion or insertion. - The following named settings for SimilarityRules implement various similarity matrices typically used for particular bioinformatics purposes:
-
"BLAST" alignment of nucleotide sequences "BLOSUM62" local alignment of related amino acid sequences "BLOSUM80" local alignment of similar sequences "PAM30" global alignment of very similar amino acid sequences "PAM70" global alignment of related sequences "PAM250" global alignment of dissimilar sequences
Examplesopen all
Basic Examples (3)
Align two strings on the first 
:
| In[1]:= |
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Align instead on the second 
by making the 
replacement favorable:
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Get the global similarity of two strings using default similarity scores:
| In[1]:= |
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Change the scores so 
and 
are considered a match:
| In[2]:= |
| Out[2]= |  |
Use the 
similarity matrix to globally align related protein sequences:
| In[1]:= |
| Out[1]= |  |
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