[BiO BB] Theoretical Scoring Matrix Question
golharam at umdnj.edu
Tue Apr 11 13:50:04 EDT 2006
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?
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
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
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University of Nevada at Reno
Dept. of Biochemistry / MS330
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