[Biopython] Restriction enzyme digestion gels

[Peter]

On Wed, Jul 29, 2009 at 11:56 AM, Peter Saffrey<pzs at dcs.gla.ac.uk> wrote:
> I want to run an "in-silico" gel, where I take a nucleotide sequence, cut it
> with an enzyme (probably using a tool like restrictionmapper):
>
> http://www.restrictionmapper.org/
>
> and then produce a picture of what the gel should look like, with bands
> where the cuts have been made. I was wondering whether biopython has any
> tools for doing this. Otherwise, I'll hack something up in matplotlib.

Biopython has a restriction digest module which should be able to take
care of the first step for you at least:
http://biopython.org/DIST/docs/cookbook/Restriction.html

There is nothing built into Biopython's graphics module for generating
fake gel images - so using matplot seems worth trying. However, I
would suggest you talk to Jose Blanca about his work first:
http://lists.open-bio.org/pipermail/biopython-dev/2009-March/005472.html
http://bioinf.comav.upv.es/svn/gelify/gelifyfsa/

Peter