[Biopython] topology of transmembrane proteins in BioPython

[Fields, Christopher J]

There was some code submitted to BioPerl a while back that does this, it's now in Lincoln's Bio-Graphics module (which uses libgd2):

    https://github.com/GMOD/Bio-Graphics/blob/master/lib/Bio/Graphics/DrawTransmembrane.pm

I recall testing it and it worked well, but it's been quite a while.  It seemed pretty straightforward if someone wanted to try porting it.

chris

On Nov 20, 2012, at 9:12 AM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> Hi Afonso,
> 
> On Tue, Nov 20, 2012 at 2:49 PM, Afonso Duarte <aduarte at itqb.unl.pt> wrote:
>> Dear All,
>> 
>> I´m a newbie in BioPython
>> 
>> I have a list of transmembrane proteins (in XML or txt format that include:
>> name/sequence number/sequence/ secondary structure prediction/
>> transmembrane regions) that I would like to draw a topology picture from.
> 
> Are these a standard file format?
> 
>> As I have a large number I would like to implement it in Biopython. Is there
>> any package/model  that allow to run this task automatically? if not (I
>> searched but did not found one that would do it), is there a graphical
>> module that can be adapted to draw such kind of files ? (i.e. just need to
>> draw rectangles / arrows and connecting lines and allow these to be fully
>> manipulated)
> 
> Do you want to draw a protein threading through a membrane?
> 
> Or would a simple linear protein diagram work, with one or more
> blocks/shapes along the length (from N terminus to C terminus),
> as often used for showing protein domains? That should be
> possible using Biopython's GenomeDiagram (normally used for
> showing genes or regions on a genome, but you could equally
> show domains or regions on a protein).
> 
> Perhaps a couple of sample images of the kind of thing you are
> thinking of would help us to guide you?
> 
> Regards,
> 
> Peter