[Bioperl-l] Getting IC & Consensus with Bio::Matrix::PSM::SiteMatrix

Edward Wijaya ewijaya at singnet.com.sg
Mon Mar 14 04:26:05 EST 2005

Dear Stefan and James,

Thanks so much for answering

On Mon, 14 Mar 2005 21:15:43 +0800, Stefan Kirov <skirov at utk.edu> wrote:

> The rules for too low are:
Got it Stef.

> I can fix this, but do you really want to get in your consensus a  
> position with proba less than 0.5?

Yes, Don't you think by default it should be that way?
Besides it'll be nice to have an *option* of how are we going to get the  

> We can easily add IC calculating method if you really need it.
Yes, we definitely need that. I think naturally we would need the  
same as e-value.

Actually I have the subroutine to compute the IC given the frequency  
You can use it to incorporate it to the module if you want, although it  
isn't a great piece of work.
I just thought it may save you time.

> Please let me know if you have further questions.
I'll save them till next time Stef ;-)


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