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) life member (LAB, Adventure Cycling, American Youth Hostels) Effective Cycling Instructor #218-ck (lapsed) Affiliations for identification only.