[Biopython] topology of transmembrane proteins in BioPython

[Afonso Duarte]

>> 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

Actually this one I'm also interested in and so far works ok, but does not
produce the topology as in my previous message .

Thank

Afonso

-----Mensagem original-----
De: Peter Cock [mailto:p.j.a.cock at googlemail.com] 
Enviada: terça-feira, 20 de Novembro de 2012 15:28
Para: Fields, Christopher J
Cc: Afonso Duarte; <biopython at lists.open-bio.org>
Assunto: Re: [Biopython] topology of transmembrane proteins in BioPython

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/Draw
> Transmembrane.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

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