Question: How to build HMM from position weight matrix?
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jespinoz20 wrote:

Is there a way to convert a position weight matrix into a HMM that I can use with HMMER. I have a (n,m) matrix where each n_i is a position along the motif, each m_j is a nucleotide in {A, T, C, G}, and each i,j is the probability nucleotide m_j occurring at n_i.

For example, the following would be a 7 bp motif. I have longer ones but I just wanted to show this for an example. How can I convert this into a HMM that can be used with HMMER?

``````0.000000  0.009876  0.990124  0.000000
0.000420  0.968691  0.000420  0.030469
0.010086  0.989704  0.000000  0.000210
0.005884  0.000630  0.003362  0.990124
0.010506  0.979828  0.009036  0.000630
0.001471  0.007144  0.008405  0.982980
0.002732  0.986132  0.010717  0.000420
``````
pwm hmm meme motif • 1.2k views
written 2.5 years ago by jespinoz20

I am not quite sure this is exactly what you need, but look at this article:

https://hal.inria.fr/hal-01244770/document

This doesn't look like a typical position weight matrix but rather a matrix of probabilities at each position. A position weight matrix corresponds to the log of the frequencies normalized to a background model. Anyway, you could view it has an HMM (the values represent emission probabilities) so convert it into HMMER's text format.

Interesting, I will check this out. I wasn't thinking about the additional fields that are left out of a probability matrix. I was naively using the terminology. So I need to have emission and transition state probabilites for a position weight matrix?