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>.

pftools 2.3                                        April 2003                                            GTOP(1)