Re: [R] Best HMM package to generate random (protein) sequences?

From: Dennis Murphy <djmuser_at_gmail.com>
Date: Tue, 22 Mar 2011 21:03:41 -0700

Hi:

I can't give you a direct answer, but I'd suggest trying

library(sos)
findFn('hidden Markov model')

which should give you a pretty good idea of where to start looking. If you don't have the package, install it first from CRAN.

HTH,
Dennis

On Tue, Mar 22, 2011 at 4:07 PM, Emmanuel Levy <emmanuel.levy_at_gmail.com>wrote:

> Dear All,
>
> I would like to generate random protein sequences using a HMM model.
> Has anybody done that before, or would you have any idea which package
> is likely to be best for that?
>
> The important facts are that the HMM will be fitted on ~3 million
> sequential observations, with 20 different states (one for each amino
> acid). I guess that 2-5 hidden states should be enough, and an order
> of 3 would also be enough I would say.
>
> Thanks a lot for any suggestion!
>
> All the best,
>
> Emmanuel
>
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