[Biopython] topology of transmembrane proteins in BioPython

[Peter Cock]

On Tue, Nov 20, 2012 at 3:23 PM, Fields, Christopher J
<cjfields at illinois.edu> wrote:
> 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

That produces images like this does it?
http://www0.cs.ucl.ac.uk/staff/T.Nugent/images/CLN3_Consensus_Labelled.png

>From here:
http://www0.cs.ucl.ac.uk/staff/T.Nugent/code.html

> On Nov 20, 2012, at 9:12 AM, Peter Cock <p.j.a.cock at googlemail.com>
>>
>> Do you want to draw a protein threading through a membrane?

See above, I was meaning something like this:
http://www0.cs.ucl.ac.uk/staff/T.Nugent/images/CLN3_Consensus_Labelled.png

>> 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).

That would give something a bit like this:
http://www0.cs.ucl.ac.uk/staff/T.Nugent/images/BACS2_NATPH_consensus.png

Again, from here:
http://www0.cs.ucl.ac.uk/staff/T.Nugent/code.html

Peter