NAME

       gtop - convert a profile in GCG format into PROSITE format

SYNOPSIS

       gtop      [  -ahls  ]  [  -E  gap_extend  ]  [  -F rescale ] [ -G gap_open ] [ -O offset ]
                 gcg_profile | - [ parameters ]

DESCRIPTION

       gtop converts a profile generated by the GCG program ProfileMake, or by a  GCG  compatible
       profile  construction  program,  into PROSITE format, and optionally rescales the profile.
       The result is written to the standard output.  On input, gtop divides all weights  of  the
       profile  by  100,  as  GCG  programs  do.  On output, profile scores are multiplied by the
       rescaling factor F and rounded to the nearest integer.  If symmetric gap weighting mode is
       chosen,  the  gap  opening weights are divided by 2 and assigned to the MI, MD, IM, and DM
       transition scores.  If asymmetric gap weighting mode is chosen, the  gap  opening  weights
       are  left  unchanged and assigned to the MI and MD transition scores only.  If no argument
       is specified, the program attempts to read the GCG formatted  profile  from  the  standard
       input.

OPTIONS

       gcg_profile
              Input  GCG profile.  If the filename is replaced by a '-', gtop will read the input
              profile from stdin.

       -a     Apply asymmetric gap weighting mode (see the description section).

       -h     Display usage help text.

       -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.

       -s     Apply symmetric gap weighting mode (default) (see the description section).

       -E gap_extend
              Gap extension penalty.
              Default: 0.05

       -F rescale
              Score rescaling factor.
              Default: 100

       -G gap_open
              Gap opening penalty.
              Default: 4.5

       -O offset
              Output  score  offset.  This  value  is  added  to  all  profile match scores after
              multiplication by the rescaling factor F.
              Default: 0

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.

       E=#    Gap extension penalty.
              Use option -E instead.

       F=#    Output score rescaling factor.
              Use option -F instead.

       G=#    Gap opening penalty.
              Use option -G instead.

       O=#    Output score offset.
              Use option -O instead.

EXAMPLES

       (1)    gtop -G 1.0 -E 1.0 -F 50 sh3.gpr | pfsearch -far - sh3.seq | sort -nr

              First converts the GCG profile 'sh3.gpr' into PROSITE  format,  then  searches  the
              protein library 'sh3.seq' with the reformatted profile to generate a sorted list of
              optimal alignment scores.  The pfsearch(1) option -r causes alignment scores to  be
              expressed  in raw score units.  'sh3.seq' contains 20 SH3 domain-containing protein
              sequences from SWISS-PROT release 32.

EXIT CODE

       On successful completion of its task, gtop 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.

BUGS

       gtop  defines  SCORE=0;  N_SCORE=0; for the mandatory cut-off level zero. These parameters
       should be changed to more reasonable values using a text editor, prior to  profile  search
       operations.

SEE ALSO

       pfsearch(1), pfscan(1), pfmake(1), sort(1)

AUTHOR

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