[Biopython] sticky ends in Biopython

[Mark Budde]

OK, that looks useful. Thanks.
-Mark


On Sun, Apr 7, 2013 at 11:05 AM, Björn Johansson <
bjorn_johansson at bio.uminho.pt> wrote:

> >
> > Message: 2
> > Date: Sat, 6 Apr 2013 17:36:10 -0700
> > From: Mark Budde <markbudde at gmail.com>
> > Subject: [Biopython] Restriction enzymes and sticky ends
> > To: biopython <biopython at lists.open-bio.org>
> > Message-ID:
> >         <
> > CAEwaGEv5pq+N2EfghiQUTjBShkt2mZXLN85kZrTcg_dJoFB86w at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi - I have a question about sticky ends in Biopython. Specifically, is
> > there any way to  maintain sticky end information? Having read the
> > restriction doc (
> http://biopython.org/DIST/docs/cookbook/Restriction.html
> > ),
> > I suspect that the answer is no. It seems that the cut sites are only
> > maintained for the top strand. So I am planning on adding this data in my
> > program (although I will need to read up on classes).
> >
> > However, this requires that I can get the cut site information. The only
> > way that I can find to extract this information is from the
> > Restriction.Enzyme.elucidate(), which gives the cut site as NN^NN_NN. I
> can
> > use this information to determine the cut sites, but I expect that there
> is
> > a more direct way, since the elucidate() function must be generating this
> > from some attribute.
> >
> > FYI, I am curious about this because I want to simulate GoldenGate
> cloning
> > in Biopython.
> >
> > Thanks,
> > Mark Budde
> >
> >
> > ------------------------------
> >
>
> Hi Mark,
>
> Check out Python-dna that have classes for dealing with
> double stranded DNA. This package depends on Biopython and a couple of
> additional modules.
>
> Disclaimer: I am the developer of Python-dna
>
> Python-dna at pypi https://pypi.python.org/pypi/python-dna/
> Source code        https://code.google.com/p/pydna/
> Documentation      http://python-dna.readthedocs.org/
> Discussion group
> https://groups.google.com/forum/?fromgroups#!forum/python-dna
>
> / Bjorn Johansson
>
>
>
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