[Biopython] pydna - sub cloning and DNA assembly built on Biopython

[Björn Johansson]

Hi all,

I would like to announce pydna which is a python package for working with
double stranded DNA.
It supports cut and paste cloning operations, PCR and simulation of DNA
assembly protocols like
Gibson assembly and homologous recombination.

DNA assembly is carried out by first construction a graph using NetworkX,
which is analyzed for all
possible circular or linear recombination products.

Check out the links below if you are interested:

Documentation https://pydna.readthedocs.org/en/latest/
PyPi repository https://pypi.python.org/pypi/pydna/
pydna group https://groups.google.com/forum/#!forum/pydna
conda package https://binstar.org/bjorn/pydna

Example:

>>> import pydna
>>> seq = pydna.Dseq("GGATCCAAA","TTTGGATCC",ovhg=0)
>>> seq
Dseq(-9)
GGATCCAAA
CCTAGGTTT
>>> from Bio.Restriction import BamHI
>>> a,b = seq.cut(BamHI)
>>> a
Dseq(-5)
G
CCTAG
>>> b
Dseq(-8)
GATCCAAA
    GTTT
>>> a+b
Dseq(-9)
GGATCCAAA
CCTAGGTTT
>>> b+a
Dseq(-13)
GATCCAAAG
    GTTTCCTAG
>>> b+a+b
Dseq(-17)
GATCCAAAGGATCCAAA
    GTTTCCTAGGTTT
>>> b+a+a
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/dist-packages/pydna/dsdna.py", line 217,
in __add__
    raise TypeError("sticky ends not compatible!")
TypeError: sticky ends not compatible!
>>>

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Björn Johansson
Assistant Professor
Departament of Biology
University of Minho
Campus de Gualtar
4710-057 Braga
PORTUGAL
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