[From nobody Thu Aug 31 10:34:04 2006
Message-ID: <44F63DB4.5030307@utk.edu>
Date: Wed, 30 Aug 2006 21:39:00 -0400
From: Stefan Kirov <skirov@utk.edu>
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To: Senduran Balasubramaniam <sendu@dev.open-bio.org>
Subject: SiteMatrix changes
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Sendu,
Perhaps I do not understand your idea, but it seems to me the changes 
you made to SiteMatrix are wrong.
Why did you have to remove the pseudo-counts? The correction can be set 
to 0 which will disable it ic case this is necessary. Pseudo counts are 
intended to account for the probabilistic uncertainty.  On the other 
hand the correction should be disabled by default if instead of raw 
count frequencies are used for the construction of the object (still 
having 0 is a bad idea). My implementation was not taking care of that 
which leads to wrong results...
Next, the rules you have enforced for the IUPAC do not make sense to me. 
For example in case the frequency for A is 0.45, G 0.45, C 0.05 and T 
0.05, according to you rules the result would be N, which makes no sense.
Would you please clarify the changes you have made or roll them back?
Thanks!
Stefan

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