Ptoh converts a PROSITE formatted generalized profile into an approximately equivalent HMMER (default) or SAM formatted hidden Markov model (HMM). The file *profile* is a nucleic acid or protein profile in PROSITE format. The random_model file contains a simple null-model in the format used by the HMM search programs of the HMMER package. The profile-to-HMM conversion method is described in Bucher et al. (1996). All profile scores corresponding to transitions which are not supported by the HMM architectures of the SAM and HMMER packages, are ignored. If no random model is specified on the command line, the null model given in the GENERAL_SPEC data block of the profile is used. If this is also missing, a flat residue distribution is assumed.
Parent program: pftools
PFTools is a collection of programs supporting the generalized profile format and search method of PROSITE.