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My end goal is a C++ implementation of

  • a Profile HMM (a profile hidden markov model is a model which contains information about a multiple sequence alignment of proteins; just providing some background as the type of model is not necessarily important for what I want to ask).
  • Baum Welch training (and implicitly Forward algorithm, Backward algorithm)

I have everything up and running as long as I don't try to use any silent states.

My biggest problem is that I do not know how to account/modify equations for silent states in my Forward/Backward algorithms. I didn't really find any good examples of this particular case online and I was wondering if anybody could give me a hint or point me in the right direction as I am not very math/stat savvy.

Follow up question: is there a user friendly package/toolbox with these algorithms already implemented? I ask this so that after I manage to complete my algos I can compare results to make sure I compute everything correctly.

I apologize if I was a bit incoherent about my problem. I will be monitoring this question and I will provide additional details as required.

share|improve this question
I saw this PDF today, it has some slides talking about silent states and how to modufy them in your code..… If you can do it, please, tell me. Thank you! – user20497 Feb 5 '13 at 18:25
Could you please provide more details? – Sven Hohenstein Feb 5 '13 at 18:53
e.g. This is the one I have experience with and it is used for bioinformatical research. There are many, many HMM implementations out there (C#, Java, python, C++, ...). Did you already search google for it and did not find something that worked for you (please specify why) or did you just not look yourself yet ;) -> sorry I just saw this post is very old, I don't know why it showed up at the top! – Verena Haunschmid Jan 3 '14 at 10:15
url is not working for me. – Verena Haunschmid Jan 3 '14 at 10:15

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