[Biopython] Sequence assembly in (bio)python

[Björn Johansson]

Hi,
My purpose is really to try to adapt the software for a different purpose. I
would like to see if an assembler program can be used to predict the outcome
of homologous recombination between DNA fragments that share small stretches
of homology. This is a method that I ofetn use to clone DNA in the lab, but
there is afaik no software where the assembled molecule can be predicted.

Thanks for the reply!
/bjorn


On Fri, Dec 3, 2010 at 09:21, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> 2010/12/3 Björn Johansson <bjorn_johansson at bio.uminho.pt>:
> > Hi,
> > I wonder if there is a sequence assembler (like phred, cap3)
> > implemented in python?
>
> Possibly, people have used Perl for this (!).
>
> > I am working on a small utility to assemble a handful of sequences
> > and in this case I think that a standalone assembler might be
> > overkill, and I would like to tweak the parameters easily.
> >
>


> > Alternatively, is there (bio)python bindings for any assembler
> > program? I could not find any in biopython.
>
> Do you mean binding in the sense of a programming API? There
> is pysam which is a Python wrapper for the samtools C-API.
>
> If you mean bindings in the sense of a command line tool wrapper,
> there is one for NovoAlign in Bio.Sequencing.Applications, and
> others could be added. I did wonder about writing one for MIRA
> but concluded it would be a never ending task since it is under
> such active development. Other assemblers should be
> easier is they have a manageable number of options.
>
> Regards,
>
> Peter
>



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Björn Johansson
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