[BiO BB] A question on Smith-Waterman algorithm

Boris Steipe boris.steipe at utoronto.ca
Thu Sep 14 13:56:55 EDT 2006

If you use a matrix that gives a positive expectation value for a  
random match, a >>local<< alignment algorithm like SW will simply  
extend the alignment into random noise, since the mismatches it  
encounters do not reduce the score.

Remember that a scoring matrix is only a tool to represent a model of  
how similarity came about. The 1/0 matrix implicitly states that  
there is information if you observe matches and no information if you  
observe mismatches. This is not a model of evolution however, since  
evolution implies that mismatches are less likely and thus should be  
penalized if two sequences are related.



On 14-Sep-06, at 12:22 PM, Skull Crossbones wrote:

> Hello all,
> In the SW algo. mismatches are given negative scores.
> Does this mean I can not use an Identity Scoring
> Matrix ( 1 for match and 0 for mismatch) for aligning
> DNA sequences? Does the term "Mismatch" applies for
> protein scoring matrices like PAM and BLOSUM
> Thanks in advance
> WoA
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