[BiO BB] Theoretical Scoring Matrix Question

[Ryan Golhar]

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?

Ryan