Ubuntu Manpage: htop - convert a HMMER ASCII-formatted HMM into an equivalent PROSITE profile

NAME

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

SYNOPSIS

       htop      [  -fhilos  ]  [  -B  norm_logbase  ]  [  -C  cut_off  ]  [ -F multiplier ] [ -H
                 init/term_score  ]  [  -L  score_logbase  ]   [   -M   nb_unprotect   ]   [   -P
                 percent_unprotect ] [ -Q odds_ratio ] hmm_file | - [ random_model ] [ parameters
                 ]

DESCRIPTION

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

OPTIONS

hmm_file
Input HMM ASCII-file. By default, htop expects a HMMER2 formatted HMM. If the
option -o is set, the file should be in HMMER1 ASCII format. If the filename is
replaced by a '-', htop will read the input HMM from stdin.

random_model
Input random model file. Only used in conjunction with HMMER1 HMMs (see option -o).
This file should contain a simple null-model using the same residue alphabet as the
hmm_file.

-f Emulate HMM fragment search (only effective with old HMMER1 format). When given as
input to the pftools programs pfsearch(1) or pfscan(1), 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.

-h Display usage help text.

-i Force all insert extension scores to be zero.

-l Remove output line length limit. Individual lines of the output profile can exceed
a length of 132 characters, removing the need to wrap them over several lines.

-o Assume input to be in old HMMER1 ASCII format. Since version 2.2, the pftools
assume by default the 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.

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

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

-F multiplier
Output score multiplier. On output, all profile scores are multiplied by this
factor and rounded to the nearest integers.
Only effective with HMMER2 format.
Default: 100

-H init/term_score
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: * (low-value)

-L score_logbase
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 nb_unprotect
Maximal number of unprotected residues at the ends of the profile.
Type: integer
Default: 5 (meaning that the protected region starts at position 6).

-P percent_unprotect
Percent profile-length at the ends of the profile, which will not be included in
the protected area.
Type: real
Default: 0 (range 0 to 100)

-Q odds_ratio
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: 0.8

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.

       B=#    Match score logarithmic base.
              Use option -B instead.

       C=#    Level zero cut-off.
              Use option -C instead.

       F=#    Output score multiplier.
              Use option -F instead.

       H=#    High-cost init/term score.
              Use option -H instead.

       L=#    Profile scores logarithmic base.
              Use option -L instead.

       M=#    Maximal number of unprotected residues.
              Use option -M instead.

       P=#    Percentage of unprotected residues.
              Use option -P instead.

       Q=#    Unknown residues odds ratio.
              Use option -Q instead.

EXAMPLES

       (1)    htop pfam_sh3.hmm > pfam_sh3.prf

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

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

              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/).

EXIT CODE

       On  successful  completion  of  its  task, htop 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.

AUTHOR

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