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

From: Emmanuel Levy <emmanuel.levy_at_gmail.com>
Date: Tue, 22 Mar 2011 19:07:29 -0400


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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