[Bioperl-l] Module to draw transmembrane protein topology

Tim Nugent t.nugent at cs.ucl.ac.uk
Tue Feb 20 09:31:20 EST 2007


Thanks Chris, glad it's appreciated.

Is there anything else I can do? If anyone has any requests/suggestions 
please let me know too.

Best wishes,

Tim

Chris Fields wrote:
> 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
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
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


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