[BioPython] (bio)python for vector cloning

[Peter]

Hi Alex,

I hope you don't mind me CC'ing this back onto the mailing list.

On Tue, Aug 12, 2008 at 10:56 AM, Alexandre Santos wrote:
>> What format will you have your raw vector sequences in?  Maybe FASTA?
> Both FASTA and GenBank formats. I think this should not be a problem

Good.

>> 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
>
> I checked the documentation and it's exactly what I need!

Good.

>> 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
>
> I mean the typical vector graphic representation that gives you an
> idea of the vector sequence structure (see for instance
> http://www.addgene.org/pgvec1?f=d&vectorid=345&cmd=genvecmap&dim=800&format=html&mtime=1187931178).
> I would use it for personal documentation, but also when I send the
> plasmids to other people.
>
> It seems GenomeDiagram could be used for that job, but not without
> some heavy customization... It would be nice to have something already
> usable for this purpose.

I have used GenomeDiagram for plasmid figures, for example showing the
location of microarray probe target sequences.  However, right now it
does lack support for "arrowed features" on the circles, and the fancy
labeling in that example.  So I would agree, recreating that figure
using Biopython and GenomeDiagram would need plenty of additional
work.  However, a simplified version would be fairly easy I think.

>> Also please be aware that some bits of the Pasteur Biopython tutorial
>> are out of date
>
> Thanks for the warning, I will mind it when I try biopython.
>
> Thanks for the help!
>
> Alex

Sure,

Peter