NAME

       htop - convert a HMMER ASCII-formatted HMM into an equivalent profile

SYNOPSIS

       htop [ -fios ] [ hmm-file | - ] [ random-model-file ] [B=#]
               [C=#] [F=#] [H=#] [L=#] [M=#] [P=#] [Q=#]

DESCRIPTION

       htop converts a hidden Markov model (HMM) into an equivalent PROSITE-formatted generalized profile.  hmm-
       file  is  a nucleic acid or protein HMM in HMMER ascii-format.  random-model-file contains a simple null-
       model in the format used by the HMM search programs of  the  HMMER1  package.   This  parameter  is  only
       effective in conjunction with the -b option. If omitted, a random model consisting of the average residue
       probabilities of the insert states will be used.

OPTIONS

       -f     Emulate  HMM  fragment search (only effective with old HMMER1 format).  When given as input to the
              pftools programs pfsearch or pfscan, the resulting profile  will  behave  like  the  original  HMM
              searched  with  the  HMMER1  program  hmmfs.   The  default  mode  is  to emulate HMM local search
              implemented in the HMMER1 program hmmls.

       -i     Force all insert extension scores to be zero.

       -o     Assume input to be in old HMMER1 format. Pftools version 2.2 assumes by default HMMER2 format.

       -s     Implement semiglobal alignment mode. This option forces  all  external  initiation  scores  to  be
              identical to the internal initiation score at the beginning of the profile. Likewise, the external
              termination  scores  are  set  to  the  value  of the internal termination score at the end of the
              profile.

ADDITIONAL PARAMETERS

       B=#    Logarithmic base to be used for normalization of profile match scores  (only  effective  with  old
              HMMER1 format).  Default: B=2.0.

       C=#    Level  zero  cut-off  value  in normalized score units.  Default: C=8.5 (C=0.0 in conjunction with
              option -o).

       F=#    Output score multiplier (only effective in conjunction with old HMMER1  format).  On  output,  all
              profile  scores are multiplied by this factor and rounded to the nearest integers. Default: F=100.
              With the new HMMER2 format, which uses an  integer-rounded  log-odds  representation  of  the  HMM
              parameters, the original values cannot be rescaled.

       H=#    High-cost  initiation/termination score (only effective in conjunction with -s option). This score
              will be applied to all external and internal initiation and  termination  scores  at  path  matrix
              positions  where  initiation  or  termination  at low cost is not possible according to semiglobal
              alignment mode.  Default: H=* (low-value).

       L=#    Logarithmic base to be used for representation of profile scores (only  effective  in  conjunction
              with old HMMER1 format).  Default: 1.0233739 (1/30 bit units).

       M=#    Maximal number of unprotected residues at the ends of the profile.  Default: M=5.

       P=#    Percent  profile-length  at  the  ends of the profile, which will not be included in the protected
              area (may be overwritten by parameter M, see above). Default: P=0.

       Q=#    Position-independent odds ratio assumed for  unknown  residues.   This  parameter  determines  the
              default  values  for profile scores M0 and I0.  Note that the I0 scores may be over-written by the
              -i option.  Default: Q=0.8.

EXAMPLES

       (1)    htop pfam_sh3.hmm > pfam_sh3.prf

              Converts the HHMER2-formatted SH3 domain profile in "pfam_sh3.hmm"  into  a  generalized  profile.
              After this conversion, the following two commands:

              hmmsearch --null2  pfam_sh3.hmm sh3.seq
              pfsearch -fy pfam_sh3.prf sh3.seq C=5.0

              should produce equivalent results in terms of raw scores and profile-sequence alignments (E-values
              and  normalized  scores  will  usually be different). Note that the program hmmsearch is from Sean
              Eddy's HMMER2 package (http://hmmer.wustl.edu/).

AUTHOR

       Philipp Bucher
       Philipp.Bucher@isrec.unil.ch

pftools 2.2                                         July 1999                                            HTOP(1)