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SOLUTIONS
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| SimilarityRules is an option for functions such as SequenceAlignment that gives a list of rules for similarity scores to assume between pairs of elements. |
, where the 
give elements to compare, and v gives their similarity.
can be either explicit characters or other elements, or patterns. 
gives the score for a deletion; a rule for 
gives the score for an insertion.
, giving a score of 
for any pair of identical elements, and a score of 
for any mismatch, deletion or insertion.| "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 |
:
by making the 
replacement favorable:
and 
are considered a match:
similarity matrix to globally align related protein sequences:
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EXAMPLES
Basic Examples 
