[BioPython] (bio)python for vector cloning

[Peter]

On Sun, Aug 10, 2008, Alexandre Santos wrote:
> Hello,
>
> I'm currently evaluating the suitability of python and biopython for
> the planning of my molecular biology chores.
>
> In particular, I would like to use for instance the ipython shell to
> pick up my vectors of interest, the list of restriction enzymes I have
> in the shelf, and design cloning strategies, plot annotated vector
> maps, etc.

What format will you have your raw vector sequences in?  Maybe FASTA?

Biopython's Bio.Restriction module (contributed by Frederic Sohm) may
be helpful.  It is documented here (separate from the main tutorial at
the moment), http://biopython.org/DIST/docs/cookbook/Restriction.html

What exactly do you mean by plot annotated vector maps?  There are
some basic graphics capabilities in Biopython which use ReportLab.
Depending on what you want to do, GenomeDiagram might be helpful too.
http://bioinf.scri.ac.uk/lp/programs.php#genomediagram

> My question is on whether anybody has experience doing this with
> python related tools? I had a look at some biopython documentation and
> tutorials (http://www.pasteur.fr/recherche/unites/sis/formation/python/apa.html#sol_digest),
> and it seems feasible, but if possible I would like some
> experience-based feedback.

I have no personal experience of doing this kind of worth with
Biopython, but it should be feasible.  If you try this, and have
suggestions for the Biopython documentation (or code) that would be
great.

Also please be aware that some bits of the Pasteur Biopython tutorial
are out of date - I did try and get in touch with the authors about
this via the help at pasteur.fr email address listed on the main page.
Maybe I should try and contact the authors directly...
http://www.pasteur.fr/recherche/unites/sis/formation/python/

Peter