[Biopython] sticky ends in Biopython

[Björn Johansson]

>
> 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>
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> CAEwaGEv5pq+N2EfghiQUTjBShkt2mZXLN85kZrTcg_dJoFB86w at mail.gmail.com>
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>
> 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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