[ssml] HMM to aa frequency

Kevin Karplus karplus at soe.ucsc.edu
Thu Jan 20 19:17:52 EST 2005

Robson asked

> Does any of you know if there is a way to build a matrix of expected
> aminoacid frequencies for each position of an HMM model, like Pfam_fs
> or Pfam_ls? I want to compare the expected aa frequencies for each
> PFam HMM model to the actual frequencies in the Pfam-A.full alignment.

Sure, just look at the model files.  The emission probabilities of the
match states are precisely the numbers you are asking for.

Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
(Senior member, IEEE)	(Board of Directors, ISCB)
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