NAME

       gtop - convert a profile in GCG format into PROSITE format

SYNOPSIS

       gtop [ -as ] [ gcg-profile ]   [G=#] [E=#] [F=#] [O=#]

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

       -a     Apply asymmetric gap weighting mode.

       -s     Apply symmetric gap weighting mode (default).

PARAMETERS

       G=#    Gap opening penalty. Default: G=4.5.

       E=#    Gap extension penalty. Default: E=0.05.

       F=#    Rescaling factor. Default: F=100.

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

EXAMPLES

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

              First converts the GCG-formatted profile in 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  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.

              See also manual pages of pfsearch and UNIX command sort.

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.

AUTHOR

       Philipp Bucher
       Philipp.Bucher@isrec.unil.ch

pftools 2.2                                       February 1998                                          GTOP(1)