Provided by: toppred_1.10-10_amd64 bug

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 bartoppred -
           toppred is able to read data from stdin.

AUTHORS

       Eric Deveaud <edeveaud@pasteur.fr>, Institut Pasteur and Katja Schuerer.