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PROGRAM:
NAME
toppred - Transmembrane topology prediction.
SYNOPSIS
toppred [options] <seq data> ...
OPTIONS
Following command line options are allowed:
-c value
Use value as certain cut-off value. Default is 1.
-d val
Use val as critical distance between 2 transmembrane segments. If 2 calculated
segments are separated by a distance smaller than val amino-acids only the segment
with best hydrophobicity value is taken in account. Default is 2.
-e switch the cyt-ext calculus to Eucaryotes. Default is Procaryotes.
-g format
Produce or display hydrophobic profile in specified format. Currently the supported
values for format are:
x11 : display the graph on screen (default).
ps : produce a .ps file.
png : produce a .png file.
ppm : produce a .ppm file.
none : no profile is produced.
Warning: this option and the related values are only available if toppred is compiled
with the gnuplot support.
-h Usage display.
-H file
Load hydrophobicity scale from file, default is GES-scale. Accepted values are
either:
KD-scale : (Kyte and Doolittle, J. Mol. Biol (1982) 157, 105-132 )
GES-scale : (Goldman Engelman Steitz Ann. Rev. Biophys. Biophys. Chem. 1986 15/ 321
53)
GVH-scale : (Gunnar von Heijne J. Mol. Biol. (1992) 225, 487-494)
either your own hydrophobicity scale file. In this case the hydrophobicity scale file
must be located in the working directory.
In order to use your own hydrophobicity scale file, see the format of the supported
scale files in the toppred data directory on your system; look in
/usr/share/toppred/or /usr/local/share/toppred/, or ask your system administrator.
-n value
Use value as a core window length, default is 11.
-o file
Place the output into file, and store all other files to the same directory than file.
-O format
Print output in the specified format. Supported values are: old: old toppred output
format, new: new toppred output format (the default value), html: produce an html page
per sequence, note that if not specified hydrophobic profile and topologies
representation are forced in png format.
-p value
Use value as putative cut-off, default is 0.6.
-q value
Use value as wedge window length, default is 5.
-s value
Use value as critical loop length. If a loop between 2 transmembrane segments has a
length greater than val the Lys/Arg ratio is not taken in account to determine the
topologies. Default is 60.
-t format
Produce images of the topologies in specified format. Currently the supported values
for format are: png: produces images of the topologies in png format, none: no graphic
representation of the topologies is produced. Default is png.
Warning: this option and the related values are only available if toppred is compiled
with the libgdb support.
-v Display the version number.
FORMAT
toppred only handles fasta sequence format as input.
toppred handles 2 output format via the -O flag.
DESCRIPTION
toppred is a program to determine the topology of a transmembrane protein based on G. von
Heijne algorithm.
"Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside
rule." J. Mol. Biol. 1992 225,487-494.
Each sequence from seq data in fasta format is processed, and toppred generate the
Hydrophobycity profile of the sequence, and the corresponding hydrophobycities values in
the file <sequence-ID>.hydro.
Furthermore, the predicted topologies are represented as png images. Each topology is
stored in file <sequence-ID>-<number>.png
The hydrophobicity profile is computed using a window formed by a core rectangular window
of size n, flanked by 2 triangular windows of size q. NB rectangular and triangular mean
that the ponderation values inside those windows are respectively constant and variable.
The hydrophobicity profile is computed using the following window
-> n <-
___________
/⎪ ⎪
/ ⎪ ⎪
/__⎪_________⎪__
-> q <- -> q <-
-> l = n + 2q <-
Thus one can use a rectangular window by setting q to 0.
toppred produces the following output files, depending on the command line options
foo.hydro
File containing the hydrophobic values for the sequence foo.
foo.ps, foo.ppm, foo.png
Image representing the hydrophobic profile for the sequence foo in postcript, ppm or
png format depending on the -g option value specified on command line, respectively -g
ps, -g ppm or -g png.
foo-1.png ... foo-n.png
Image representing the graphic representation of the predicted topology 1... n for the
sequence foo in png format if the -t png option is given on the command line.
ENVIRONMENT
TOPPREDDATA could be used to specify an alternate toppred data folder
EXAMPLES
Consider the fasta formated sequence foo in file bar.
toppred bar
Process all sequences in fasta format from bar, display for each sequence the
hydrophobicity profile, produce the corresponding foo.hydro and the corresponding
foo-<#>.png graphical topologies representation as png images.
toppred -g ps bar
Same as previous, except that instead of displaying the hydrophobicity profile on
screen, this one is produced in a postcript format image foo.ps
toppred -g none bar
Same a previous, except that the hydrophobicity profile is not displayed neither
produced.
toppred -g none -t none bar
Same a previous, except that neither the hydrophobicity profile neither the graphical
topologies representation are not produced
toppred -H KD-scale bar
Use KD scale instead of default GES scale, while processing sequences.
toppred -O html -g png -t none -o result bar
Write html outpout in file result, furthermore the hydrophobicity profile is produced
in PNG format and graphics topologies are not produced.
cat bar ⎪ toppred -
toppred is able to read data from stdin.
AUTHORS
Eric Deveaud <edeveaud@pasteur.fr>, Institut Pasteur and Katja Schuerer.
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