[Bioperl-l] SiteMatrix changes

Stefan Kirov stefan.kirov at bms.com
Thu Aug 31 10:00:08 EDT 2006

This may be a double posting- I think I am having troubles with my SMTP. 

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 in 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
counts frequencies are used for the construction of the object (still
having 0 is a bad idea, but this is now user's responsibility). 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 to 
1.32 (same with tests)? After that we can fix the pseudo counts for 
freq/log object creation.
Stefan Kirov

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