[BiO BB] Theoretical Scoring Matrix Question

Martin Gollery marty.gollery at gmail.com
Tue Apr 11 13:40:53 EDT 2006

Hi Ryan,

Pick a number of sequence pairings, some where you know that the sequences
are related and some where you know that they are not related. Your matrices
should hopefully provide better discrimination than ednafull or BLAST, that
is, they should provide more positive scores for the true positives and more
negative scores for the known negatives. You need to do this on a large
number of sequences to get a good picture- one or two is not enough.


On 4/11/06, Ryan Golhar <golharam at umdnj.edu> wrote:
> 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
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Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
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