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