Determinig the number of hidden states in a Hidden Markov Model

Question

[Tamador]

I am learning about Hidden Markov Model to detect more members of the gene family by scanning the genome with the profile-HMM , so I need to know how do I determine the number of hidden states in HMM profile ??

Thanks

Answer 1

[Sinji]

Typically, you would run N number of chromatin states and then manually annotate them, and see which one best fits the data, similarly to K-means clustering. There may be a more automated way as there is for K-means, but not one I am immediately familiar with.