R help - Mar 2011 - Best HMM package to generate random (protein) sequences?

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

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@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
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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