[Bioperl-l] Module to draw transmembrane protein topology

Chris Fields cjfields at uiuc.edu
Tue Feb 20 09:40:38 EST 2007


You can add the module and test code (the script) to bugzilla:

http://www.bioperl.org/wiki/Bugs
http://bugzilla.open-bio.org/

Basically file a new bug report but note that it in an enhancement  
request when filling it out.  Attach the code and test script to the  
report after it is generated (note that it may be easier to add all  
of the files together as a zipped archive).  I think you could also  
add the graphical output as a binary file if they are huge files.

chris

On Feb 20, 2007, at 8:31 AM, Tim Nugent wrote:

> 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

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





More information about the Bioperl-l mailing list