gtop - convert a profile in GCG format into PROSITE format
gtop [ -ahls ] [ -E gap_extend ] [ -F rescale ] [ -G
gap_open ] [ -O offset ] gcg_profile | - [ parame-
gtop converts a profile generated by the GCG program Pro-
fileMake, or by a GCG compatible profile construction pro-
gram, into PROSITE format, and optionally rescales the pro-
file. 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 inte-
ger. 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.
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 descrip-
-h Display usage help text.
-l Remove output line length limit. Individual lines of
the output profile can exceed a length of 132 charac-
ters, removing the need to wrap them over several
-s Apply symmetric gap weighting mode (default) (see the
Gap extension penalty.
Score rescaling factor.
Gap opening penalty.
Output score offset. This value is added to all profile
match scores after multiplication by the rescaling fac-
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.
(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.
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.
gtop defines SCORE=0; N_SCORE=0; for the mandatory cut-off
level zero. These parameters should be changed to more rea-
sonable values using a text editor, prior to profile search
pfsearch(1), pfscan(1), pfmake(1), sort(1)
The pftools package was developped by Philipp Bucher.
Any comments or suggestions should be addressed to