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It may better to move the question here.

I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to generate noisy copies of the consensus sequence of different lengths. There is a figure show the process: enter image description here

I am familiar with the machine learning or graphical model. To build the HMM, we need to set the model parameter, which we learn from the training data in ML. My question is whether the train&testing works for this question? If so where can I find data to training this HMM model?

It seems Professor Richard Durbin may release some dataset. But how can I find available datasets? I lost in the bio-vocabulary and fail to find datasets. Also I am wondering whether or not this topic is very minor in this community?

Update: Since I may abuse the vocabulary, it may be better to post the original word I read. enter image description here

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    $\begingroup$ Why don't you just build an MSA (with MAFFT/MUSCLE/CLUSTAL-OMEGA) and then build a pHMM with HMMER3? Or if you want already existing HMMs, checkout PFAM $\endgroup$ – Chris_Rands May 22 at 8:47

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