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Can anyone help me with Multiple Sequence Alignment (MSA) using Hidden Markov Model (HMM) by giving an example or a reference except these 2 references:

1-Eddy, Sea.R., et al.Multiple alignment using hidden markov models, 2-Boer Jonas, Multiple alignment using hidden Markov models, Seminar Hot Topics in Bioinformatics.

I know that there are 3 states: match, deletion and insertion and I know the emission probabilities and transitions probabilities can be learned by viterbi algorithm but what is vague is that if I want to do multiple alignment I need to have HMM and if I want to have HMM I need to have aligned sequences but we know that sequences are unaligned and also with simulated annealing we can Enter randomness to the model and have better solutions and also this algorithm is different with E-M algorithm and I have another question how many states our model of HMM for this problem should have at the first step, does the number of states change during the time of convergence or it is fixed from the first??

If anybody can help me to understand what really happens in this MSA with HMM I'll appreciate.

I should explain that there have been found more sequences of DNA,RNA and protein but there are less information about structures and functions of each protein so we do MSA to understand the similarities between sequences and find out whether they are homologous (have a same ancestor) or not and find out the unknown structure and functions of sequences.

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  • $\begingroup$ What research have you done? What have you found so far? It sounds like you have already found two resources that might be relevant. Can you edit your question to give full references to those resources, including title, authors, where published, and a link if available? This might be helpful to anyone with the same question who stumbles across your question. It helps to make your question interesting for others by providing some background knowledge and approach the site from a spirit of knowledge sharing. Can you give a self-contained definition of "multiple sequence alignment"? $\endgroup$
    – D.W. ♦
    Apr 10 '17 at 22:45
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part of this question already has an answer in multiple sequence alignment using HMM and simulated annealing and about the number of states in HMM it is a challenge yet.

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    $\begingroup$ Can you summarize the answer there? $\endgroup$
    – Yuval Filmus
    Jul 20 '17 at 15:46

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