[Biopython] topology of transmembrane proteins in BioPython

[Peter Cock]

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