[Biopython] topology of transmembrane proteins in BioPython
Senthil Kumar M
senthil.debian at gmail.com
Tue Nov 20 20:00:24 UTC 2012
On Tue, Nov 20, 2012 at 8:44 AM, Afonso Duarte <aduarte at itqb.unl.pt> wrote:
>>>Are these a standard file format?
> 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
> tEaW7MP-M1MG-GXgfwZfRY_UI0ZvYAQ or here the top scheme
> 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
Although not related to Biopython/BioPerl, TeXtopo, a LaTeX package,
can plot membrane protein topology:
It accepts SwissProt, HMMTop, among other formats.
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