[Biopython] topology of transmembrane proteins in BioPython

[Afonso Duarte]

>>Are these a standard file format?

Yes

"
name
Seq number
Seq aa
TM prediction
2rd structure prediction
"


>>>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?

I would prefer a protein threading with a membrane, however for sake of
simplicity a simple linear diagram works (with blocks)

An example of what I mean can be found here
(https://encrypted-tbn2.gstatic.com/images?q=tbn:ANd9GcRgPji7TNWY0ta2_yHYYT_
tEaW7MP-M1MG-GXgfwZfRY_UI0ZvYAQ or here the top scheme
https://encrypted-tbn2.gstatic.com/images?q=tbn:ANd9GcSA8gm35RO0qBEQ-F_aHBqj
eUgWOH_uOdL8WsAFufaMEjdUNzybfA) the presence of the membrane is interesting
of course but I would survive without it.

I will also have a look at GenomeDiagram

Thanks!

Afonso

-----Mensagem original-----
De: Peter Cock [mailto:p.j.a.cock at googlemail.com] 
Enviada: terça-feira, 20 de Novembro de 2012 15:12
Para: Afonso Duarte
Cc: biopython at lists.open-bio.org
Assunto: Re: [Biopython] topology of transmembrane proteins in BioPython

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

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