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