=pod

=head1 NAME

=over 4

=item B<toppred> - Transmembrane topology prediction.

=back

=head1 SYNOPSIS

=over 4

=item B<toppred> [options] E<lt>F<seq data>E<gt> ...

=back

=head1 OPTIONS

Following command line options are allowed:

=over 4

=item -c F<value>

Use F<value> as certain cut-off value. Default is 1.

=item -d F<val>

Use F<val> as critical distance between 2 transmembrane segments.
If 2 calculated segments are separated by a distance smaller than
F<val> amino-acids only the segment with best hydrophobicity value is
taken in account. Default is 2.

=item -e

switch the cyt-ext calculus to Eucaryotes. Default is Procaryotes.

=item -g F<format>

Produce or display hydrophobic profile in specified F<format>.
Currently the supported values for format are:

=over 1

=item B<x11>  : display the graph on screen (default).

=item B<ps>   : produce a .ps file.

=item B<png>  : produce a .png file.

=item B<ppm>  : produce a .ppm file.

=item B<none> : no profile is produced.

=back

B<Warning:> this option and the related values are B<only> available
if toppred is compiled with the gnuplot support.

=item -h

Usage display.

=item -H F<file>

Load hydrophobicity scale from F<file>, default is GES-scale.
Accepted values are either:

=over 1

=item B<KD-scale>  : (Kyte and Doolittle, J. Mol. Biol (1982) 157, 105-132 )

=item B<GES-scale> : (Goldman Engelman Steitz Ann. Rev. Biophys. Biophys. Chem. 1986 15/ 321 53)

=item B<GVH-scale> : (Gunnar von Heijne J. Mol. Biol. (1992) 225, 487-494)

=item either your own hydrophobicity scale file. In this case the
hydrophobicity scale file must be located in the working directory.

=back

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 F</usr/share/toppred/>or F</usr/local/share/toppred/>,
or ask your system administrator.

=item -n F<value>

Use F<value> as a core window length, default is 11.

=item -o F<file>

Place the output into F<file>, and store all other files to the same
directory than F<file>.

=item -O F<format>

Print output in the specified F<format>. Supported values are: B<old>:
old toppred output format, B<new>: new toppred output format (the
default value), B<html>: produce an html page per sequence, note that
if not specified hydrophobic profile and topologies representation are
forced in png format.

=item -p F<value>

Use F<value> as putative cut-off, default is 0.6.

=item -q F<value>

Use F<value> as wedge window length, default is 5.

=item -s F<value>

Use F<value> as critical loop length. If a loop between 2
transmembrane segments has a length greater than F<val> the Lys/Arg
ratio is not taken in account to determine the topologies. Default is
60.

=item -t F<format>

Produce images of the topologies in specified F<format>. Currently the
supported values for format are: B<png>: produces images of the
topologies in png format, B<none>: no graphic representation of the
topologies is produced. Default is png.

B<Warning:> this option and the related values are B<only> available
if toppred is compiled with the libgdb support.

=item -v

Display the version number.

=back

=head1 FORMAT

B<toppred> only handles fasta sequence format as input.

B<toppred> handles 2 output format via the B<-O> flag.


=head1 DESCRIPTION

B<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 F<seq data> in fasta format is processed, and
B<toppred> generate the Hydrophobycity profile of the sequence, and
the corresponding hydrophobycities values in the file
E<lt>B<sequence-ID>E<gt>B<.hydro>.

Furthermore, the predicted topologies are represented as png images.
Each topology is stored in file
E<lt>B<sequence-ID>E<gt>B<->E<lt>B<number>E<gt>B<.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.

B<toppred> produces the following output files, depending on the
command line options

=over 4

=item B<foo.hydro>

File containing the hydrophobic values for the sequence B<foo>.

=item B<foo.ps>, B<foo.ppm>, B<foo.png>

Image representing the hydrophobic profile for the sequence B<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.

=item B<foo-1.png> ... B<foo-n.png>

Image representing the graphic representation of the predicted
topology B<1>... B<n> for the sequence B<foo> in png format if the -t
png option is given on the command line.

=back

=head1 ENVIRONMENT

B<TOPPREDDATA> could be used to specify an alternate toppred data
folder

=head1 EXAMPLES

Consider the fasta formated sequence B<foo> in file B<bar>.

=over 4

=item B<toppred> F<bar>

Process all sequences in fasta format from F<bar>, display for each
sequence the hydrophobicity profile, produce the corresponding
B<foo.hydro> and the corresponding B<foo>B<->E<lt>B<#>E<gt>B<.png>
graphical topologies representation as png images.

=item B<toppred> -g ps F<bar>

Same as previous, except that instead of displaying the hydrophobicity
profile on screen, this one is produced in a postcript format image
B<foo.ps>

=item B<toppred> -g none F<bar>

Same a previous, except that the hydrophobicity profile is not
displayed neither produced.

=item B<toppred> -g none -t none F<bar>

Same a previous, except that neither the hydrophobicity profile
neither the graphical topologies representation are not produced

=item B<toppred> -H KD-scale F<bar>

Use KD scale instead of default GES scale, while processing sequences.

=item B<toppred> -O html -g png -t none -o result F<bar>

Write html outpout in file F<result>, furthermore the hydrophobicity
profile is produced in PNG format and graphics topologies are not
produced.

=item cat F<bar> | B<toppred> -

B<toppred> is able to read data from stdin.

=back

=head1 AUTHORS

Eric Deveaud E<lt>edeveaud@pasteur.frE<gt>, Institut Pasteur and
Katja Schuerer.

=cut
