[BiO BB] Theoretical Scoring Matrix Question

Ryan Golhar golharam at umdnj.edu
Tue Apr 11 11:29:04 EDT 2006

I've constructed a few scoring matrices for DNA sequence based on
certain information.  I'm now trying to determine how well they perform
compared to the standard statistically based matrices, such as EDNAFULL
(+5/-4) and the standard scoring matrix used by BLAST (+1/-3).  

My question is, what would be a valid test to compare matrices against
each other?


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