NAME

       ptoh - converts a PROSITE formatted profile into an approximately equivalent HMM

SYNOPSIS

       ptoh      [  -fFhs ] [ -D del_to_del ] [ -I ins_to_ins ] [ -L log_base ] [ profile | - ] [
                 random_model ] [ parameters ]

DESCRIPTION

       ptoh converts a PROSITE formatted generalized profile  into  an  approximately  equivalent
       HMMER1  (default)  or  SAM  formatted  hidden Markov model (HMM).  The file 'profile' is a
       nucleic acid or protein profile in PROSITE format.  If  '-'  is  specified  instead  of  a
       filename,  the  profile is read from the standard input.  The random_model file contains a
       simple null-model in the format used by the HMM search programs  of  the  HMMER1  package.
       The result is written to the standard output.

       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 HMMER1 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.

OPTIONS

       profile
              Input  PROSITE  generalized  profile.   The  motif described by the profile will be
              converted into an approximately equivalent HMM. If the filename is  replaced  by  a
              '-', ptoh will read the input profile from stdin.

       random_model
              Input random model file.
              This file should contain a simple null-model using the same residue alphabet as the
              profile.

       -f     Generate free insert-modules (FIMs) at the beginning and at the end  of  the  model
              which approximately emulate domain-global or semi-global alignment mode (see Bucher
              et al.  1996).

       -F     Generate free insert-modules (FIMs) at the beginning and at the end  of  the  model
              which approximately emulate local alignment mode.

       -h     Display usage help text.

              Note:  The  meaning  of this option has changed between version 2.2 and the current
                     release of the pftools package. No option is needed  to  get  HMMER1  output
                     format because it is the default (see option -s).

       -s     Output in SAM format.

       -D del_to_del
              Delete-to-delete transition probabilities.
              They  are  used  in  conjunction  with  FIMs  (options -f, -F).  This value will be
              imposed on all delete-to-delete transitions  of  the  model.   The  other  outgoing
              transitions  from  the  affected  delete states will be renormalized to satisfy the
              "sum to one" requirement.  Note that the application of the  D  parameter  precedes
              the  application  of  the  I  parameter.   Delete-to-delete  probabilities  at  the
              beginning and at the end of the  model  may  thus  change  again  as  a  result  of
              renormalizations following the application of the I parameter.
              Default: 0.9

       -I ins_to_ins
              Insert-to-insert transition probabilities.
              They  are  used  in  the  FIMs (options -f, -F).  This value will be imposed on the
              first and the last match-to-insert and insert-to-insert transition probabilities of
              the  model.   The  other  outgoing  transitions  of  the  affected  states  will be
              renormalized such as to satisfy the "summing to one" requirement.  If the -F option
              is simultaneously set, the I parameter will also be imposed on the insert-to-delete
              transition probability at the beginning, and  on  the  delete-to-insert  transition
              probability at the end of the model.
              Default: 0.99

       -L log_base
              Logarithmic base.
              Specifies  the  logarithmic base used for conversion of the profile scores into HMM
              probabilities (The profile scores are interpreted as log-odds ratios, see Bucher et
              al.   1996).  This  value  over-writes  the  logarithmic  base specified within the
              profile by the optional LOG_BASE parameter.
              Default: 1.0233739 (1/30 bit units)

PARAMETERS

       Note:  for backwards compatibility, release 2.3 of the  pftools  package  will  parse  the
              version 2.2 style parameters, but these are deprecated and the corresponding option
              (refer to the options section) should be used instead.

       D=#    Delete-to-delete transition probabilities.
              Use option -D instead.

       I=#    Insert-to-insert transition probabilities.
              Use option -I instead.

       L=#    Logarithmic base.
              Use option -L instead.

EXAMPLES

       (1)    ptoh -Fs -L 1.0233739 sh3.prf standard.random > sh3.hmm

              Generates a SAM formatted HMM for the SH3 domain from a profile. The file 'sh3.prf'
              contains the source profile in PROSITE format.  The file 'standard.random' contains
              the null-model used for conversion of the log-odds ratios into probabilities.   The
              logarithmic  base  1.0233739  corresponds  to  1/30 bits, the implicit scale of the
              profile.  The -F option causes the HMM to emulate local alignment (fragment search)
              mode.

EXIT CODE

       On  successful  completion  of  its  task, ptoh will return an exit code of 0. If an error
       occurs, a diagnostic message will be output on standard error and the exit  code  will  be
       different  from 0. When conflicting options where passed to the program but the task could
       nevertheless be completed, warnings will be issued on standard error.

REFERENCES

       Bucher P, Karplus K, Moeri N & Hofmann, K. (1996).   A  flexible  motif  search  technique
       based on generalized profiles.  Comput. Chem.  20:3-24.

AUTHOR

       The pftools package was developed by Philipp Bucher.
       Any comments or suggestions should be addressed to <pftools@sib.swiss>.