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.\" ========================================================================
.\"
.IX Title "TOPPRED 1"
.TH TOPPRED 1 "2008-05-06" "Unix" "User Manuals"
.SH "NAME"
.IP "\fBtoppred\fR \- Transmembrane topology prediction." 4
.IX Item "toppred - Transmembrane topology prediction."
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.PD 0
.IP "\fBtoppred\fR [options] <\fIseq data\fR> ..." 4
.IX Item "toppred [options] <seq data> ..."
.PD
.SH "OPTIONS"
.IX Header "OPTIONS"
Following command line options are allowed:
.IP "\-c \fIvalue\fR" 4
.IX Item "-c value"
Use \fIvalue\fR as certain cut-off value. Default is 1.
.IP "\-d \fIval\fR" 4
.IX Item "-d val"
Use \fIval\fR as critical distance between 2 transmembrane segments.
If 2 calculated segments are separated by a distance smaller than
\&\fIval\fR amino-acids only the segment with best hydrophobicity value is
taken in account. Default is 2.
.IP "\-e" 4
.IX Item "-e"
switch the cyt-ext calculus to Eucaryotes. Default is Procaryotes.
.IP "\-g \fIformat\fR" 4
.IX Item "-g format"
Produce or display hydrophobic profile in specified \fIformat\fR.
Currently the supported values for format are:
.RS 4
.IP "\fBx11\fR  : display the graph on screen (default)." 1
.IX Item "x11  : display the graph on screen (default)."
.PD 0
.IP "\fBps\fR   : produce a .ps file." 1
.IX Item "ps   : produce a .ps file."
.IP "\fBpng\fR  : produce a .png file." 1
.IX Item "png  : produce a .png file."
.IP "\fBppm\fR  : produce a .ppm file." 1
.IX Item "ppm  : produce a .ppm file."
.IP "\fBnone\fR : no profile is produced." 1
.IX Item "none : no profile is produced."
.RE
.RS 4
.PD
.Sp
\&\fBWarning:\fR this option and the related values are \fBonly\fR available
if toppred is compiled with the gnuplot support.
.RE
.IP "\-h" 4
.IX Item "-h"
Usage display.
.IP "\-H \fIfile\fR" 4
.IX Item "-H file"
Load hydrophobicity scale from \fIfile\fR, default is GES\-scale.
Accepted values are either:
.RS 4
.IP "\fBKD-scale\fR  : (Kyte and Doolittle, J. Mol. Biol (1982) 157, 105\-132 )" 1
.IX Item "KD-scale  : (Kyte and Doolittle, J. Mol. Biol (1982) 157, 105-132 )"
.PD 0
.IP "\fBGES-scale\fR : (Goldman Engelman Steitz Ann. Rev. Biophys. Biophys. Chem. 1986 15/ 321 53)" 1
.IX Item "GES-scale : (Goldman Engelman Steitz Ann. Rev. Biophys. Biophys. Chem. 1986 15/ 321 53)"
.IP "\fBGVH-scale\fR : (Gunnar von Heijne J. Mol. Biol. (1992) 225, 487\-494)" 1
.IX Item "GVH-scale : (Gunnar von Heijne J. Mol. Biol. (1992) 225, 487-494)"
.IP "either your own hydrophobicity scale file. In this case the hydrophobicity scale file must be located in the working directory." 1
.IX Item "either your own hydrophobicity scale file. In this case the hydrophobicity scale file must be located in the working directory."
.RE
.RS 4
.PD
.Sp
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 \fI/usr/share/toppred/\fRor \fI/usr/local/share/toppred/\fR,
or ask your system administrator.
.RE
.IP "\-n \fIvalue\fR" 4
.IX Item "-n value"
Use \fIvalue\fR as a core window length, default is 11.
.IP "\-o \fIfile\fR" 4
.IX Item "-o file"
Place the output into \fIfile\fR, and store all other files to the same
directory than \fIfile\fR.
.IP "\-O \fIformat\fR" 4
.IX Item "-O format"
Print output in the specified \fIformat\fR. Supported values are: \fBold\fR:
old toppred output format, \fBnew\fR: new toppred output format (the
default value), \fBhtml\fR: produce an html page per sequence, note that
if not specified hydrophobic profile and topologies representation are
forced in png format.
.IP "\-p \fIvalue\fR" 4
.IX Item "-p value"
Use \fIvalue\fR as putative cut\-off, default is 0.6.
.IP "\-q \fIvalue\fR" 4
.IX Item "-q value"
Use \fIvalue\fR as wedge window length, default is 5.
.IP "\-s \fIvalue\fR" 4
.IX Item "-s value"
Use \fIvalue\fR as critical loop length. If a loop between 2
transmembrane segments has a length greater than \fIval\fR the Lys/Arg
ratio is not taken in account to determine the topologies. Default is
60.
.IP "\-t \fIformat\fR" 4
.IX Item "-t format"
Produce images of the topologies in specified \fIformat\fR. Currently the
supported values for format are: \fBpng\fR: produces images of the
topologies in png format, \fBnone\fR: no graphic representation of the
topologies is produced. Default is png.
.Sp
\&\fBWarning:\fR this option and the related values are \fBonly\fR available
if toppred is compiled with the libgdb support.
.IP "\-v" 4
.IX Item "-v"
Display the version number.
.SH "FORMAT"
.IX Header "FORMAT"
\&\fBtoppred\fR only handles fasta sequence format as input.
.PP
\&\fBtoppred\fR handles 2 output format via the \fB\-O\fR flag.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBtoppred\fR is a program to determine the topology of a transmembrane
protein based on G. von Heijne algorithm.
.PP
\&\*(L"Membrane protein structure prediction. Hydrophobicity analysis
and the positive-inside rule.\*(R"
J. Mol. Biol. 1992 225,487\-494.
.PP
Each sequence from \fIseq data\fR in fasta format is processed, and
\&\fBtoppred\fR generate the Hydrophobycity profile of the sequence, and
the corresponding hydrophobycities values in the file
<\fBsequence-ID\fR>\fB.hydro\fR.
.PP
Furthermore, the predicted topologies are represented as png images.
Each topology is stored in file
<\fBsequence-ID\fR>\fB\-\fR<\fBnumber\fR>\fB.png\fR
.PP
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. \s-1NB\s0 rectangular and triangular mean that the ponderation values
inside those windows are respectively constant and variable.
.PP
The hydrophobicity profile is computed using the following window
.PP
.Vb 7
\&        ->     n     <-
\&          ___________
\&         /|         |\e
\&        / |         | \e
\&       /__|_________|__\e
\&     -> q  <-     -> q  <-
\&     ->   l = n + 2q    <-
.Ve
.PP
Thus one can use a rectangular window by setting q to 0.
.PP
\&\fBtoppred\fR produces the following output files, depending on the
command line options
.IP "\fBfoo.hydro\fR" 4
.IX Item "foo.hydro"
File containing the hydrophobic values for the sequence \fBfoo\fR.
.IP "\fBfoo.ps\fR, \fBfoo.ppm\fR, \fBfoo.png\fR" 4
.IX Item "foo.ps, foo.ppm, foo.png"
Image representing the hydrophobic profile for the sequence \fBfoo\fR in
postcript, ppm or png format depending on the \-g option value
specified on command line, respectively \-g ps, \-g ppm or \-g png.
.IP "\fBfoo\-1.png\fR ... \fBfoo\-n.png\fR" 4
.IX Item "foo-1.png ... foo-n.png"
Image representing the graphic representation of the predicted
topology \fB1\fR... \fBn\fR for the sequence \fBfoo\fR in png format if the \-t
png option is given on the command line.
.SH "ENVIRONMENT"
.IX Header "ENVIRONMENT"
\&\fB\s-1TOPPREDDATA\s0\fR could be used to specify an alternate toppred data
folder
.SH "EXAMPLES"
.IX Header "EXAMPLES"
Consider the fasta formated sequence \fBfoo\fR in file \fBbar\fR.
.IP "\fBtoppred\fR \fIbar\fR" 4
.IX Item "toppred bar"
Process all sequences in fasta format from \fIbar\fR, display for each
sequence the hydrophobicity profile, produce the corresponding
\&\fBfoo.hydro\fR and the corresponding \fBfoo\fR\fB\-\fR<\fB#\fR>\fB.png\fR
graphical topologies representation as png images.
.IP "\fBtoppred\fR \-g ps \fIbar\fR" 4
.IX Item "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
\&\fBfoo.ps\fR
.IP "\fBtoppred\fR \-g none \fIbar\fR" 4
.IX Item "toppred -g none bar"
Same a previous, except that the hydrophobicity profile is not
displayed neither produced.
.IP "\fBtoppred\fR \-g none \-t none \fIbar\fR" 4
.IX Item "toppred -g none -t none bar"
Same a previous, except that neither the hydrophobicity profile
neither the graphical topologies representation are not produced
.IP "\fBtoppred\fR \-H KD-scale \fIbar\fR" 4
.IX Item "toppred -H KD-scale bar"
Use \s-1KD\s0 scale instead of default \s-1GES\s0 scale, while processing sequences.
.IP "\fBtoppred\fR \-O html \-g png \-t none \-o result \fIbar\fR" 4
.IX Item "toppred -O html -g png -t none -o result bar"
Write html outpout in file \fIresult\fR, furthermore the hydrophobicity
profile is produced in \s-1PNG\s0 format and graphics topologies are not
produced.
.IP "cat \fIbar\fR | \fBtoppred\fR \-" 4
.IX Item "cat bar | toppred -"
\&\fBtoppred\fR is able to read data from stdin.
.SH "AUTHORS"
.IX Header "AUTHORS"
Eric Deveaud <edeveaud@pasteur.fr>, Institut Pasteur and
Katja Schuerer.