[BiO BB] Theoretical Scoring Matrix Question

[Ryan Golhar]

Do you think a percent identity comparison be useful?  In other words,
how often does matrix A give a higher percent identity than matrix B?
 
 
 
 -----Original Message-----
From: Martin Gollery [mailto:marty.gollery at gmail.com] 
Sent: Tuesday, April 11, 2006 1:41 PM
To: golharam at umdnj.edu; The general forum at Bioinformatics.Org
Subject: Re: [BiO BB] Theoretical Scoring Matrix Question


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. 

Best,
Marty



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
775-784-7042
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