[Biopython] topology of transmembrane proteins in BioPython

[Senthil Kumar M]

On Tue, Nov 20, 2012 at 8:44 AM, Afonso Duarte <aduarte at itqb.unl.pt> wrote:
>>>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
>

Hi Afonso,

Although not related to Biopython/BioPerl, TeXtopo, a LaTeX package,
can plot membrane protein topology:
http://www.uni-kiel.de/pharmazie/chem/Prof_Beitz/textopo.htm

It accepts SwissProt, HMMTop, among other formats.

HTH,

Senthil