[Bioperl-l] Module to draw transmembrane protein toplogoy

Chris Fields cjfields at uiuc.edu
Mon Feb 19 16:24:04 EST 2007


I think this is pretty nice!  We can add the code and test script to  
bugzilla and (if someone has time) try to see where it might fit in,  
though Bio::Graphics sounds like a good spot.

Anyone else have ideas on where this could go?

chris

On Feb 19, 2007, at 11:29 AM, Tim Nugent wrote:

> Hi everyone,
>
> I've written a perl module to display transmembrane protein topology
> using GD. There are various options, including labels, helix/loop
> dimensions, colour schemes etc but it only requires a string or array
> containing the protein topology (e.g. transmembrane helix start/stop
> points). It produces output like this:
>
> http://www.cs.ucl.ac.uk/staff/T.Nugent/images/blue.png
> http://www.cs.ucl.ac.uk/staff/T.Nugent/images/yellow.png
>
> using the code at the bottom.
>
> Here is a the module:
> http://www.cs.ucl.ac.uk/staff/T.Nugent/source/DrawTransmembrane.pm
>
> I've never submitted anything to Bioperl before - is this sort of  
> thing
> likely to be of use to others? I imagine it would sit alongside  
> some of
> the Bio::Graphics stuff.
>
> Best wishes,
>
> Tim
>
> #!/usr/bin/perl
>
> use strict;
> use warnings;
> use lib '/scratch0/NOT_BACKED_UP/tnugent/perl5lib'; ## path to module
> use DrawTransmembrane;
>
> my @topology = (20,45,59,70,86,109,145,168,194,220);
>
> my %labels = ('5' => '5 - Sulphation Site',
>                '21' => '1st Helix',
>                '47' => '40 - Mutation',
>                '60' => 'Voltage Sensor',
>                '72' => '72 - Mutation 2',
>                '73' => '73 - Mutation 3',
>                '138' => '138 - Glycosylation Site',
>                '170' => '170 - Phosphorylation Site',
>                '200' => 'Last Helix');
>
> my $im = DrawTransmembrane->draw_transmembrane(-title => 'This is a
> cartoon displaying transmembrane helices.',
>                                                 -topology =>  
> \@topology,
>                                                 -n_terminal => 'out',
>                                                 -helix_width => 48,
>                                                 -helix_height => 125,
>                                                 -short_loop_limit  
> => 10,
>                                                 -long_loop_limit =>  
> 35,
>                                                 -loop_width => 25,
>                                                 -colour_scheme =>  
> 'yellow',
>                                                 -labels => \%labels,
>                                                 -text_offset => -10);
>
> ## print the .png file
> my $output = 'test.png';
> open(OUTPUT, ">$output");
> binmode OUTPUT;
> print OUTPUT $im->png;
> close OUTPUT;
>
> my $system = `display $output`;
>
> -- 
> Tim Nugent (MRes)
> Research Student
> Bioinformatics Unit
> Department of Computer Science
> University College London
> Gower Street
> London WC1E 6BT
> Tel: 020-7679-0410
> t.nugent at ucl.ac.uk
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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