NAME

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

SYNOPSIS

       ptoh [ -fFhs ] [ profile-file | - ] [ random-model-file ] [L=#]
               [I=#] [D=#]

DESCRIPTION

       ptoh  converts  a  PROSITE-formatted generalized profile into an approximately equivalent HMMER1- or SAM-
       formatted hidden Markov model (HMM).  profile-file is a  nucleic  acid  or  protein  profile  in  PROSITE
       format.   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

       -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     Output in HMMER1 ascii format. This is the default.

       -s     Output in SAM format.

ADDITIONAL PARAMETERS

       D=#    Delete-to-delete transition probabilities 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: D=0.9.

       I=#    Insert-to-insert transition probabilities used in the FIMs ( see 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: I=0.99.

       L=#    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).

EXAMPLES

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

              Generates a SAM-formatted HMM for the SH3 domain from a  profile.   sh3.prf  contains  the  source
              profile  in  PROSITE  format.   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.

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

       Philipp Bucher
       Philipp.Bucher@isrec.unil.ch

pftools 2.2                                       February 1998                                          PTOH(1)