[Biopython-dev] Gsoc 2014 aspirant

[Harsh Beria]

I can work on pairwise sequence alignment. Actually, I have previously
worked on this using Dynamic programming. But I doubt whether this can be a
GSOC project because the work load will not be too much. If we use
different methods to predict sequence alignment and make a front-end which
allows the user to input the sequence or even a pdb file and method of
alignment and predict the alignment, the work can be substantial enough.

Also, as suggested by Christopher, sequence alignment is pretty basic and
we can use C backend, which can significantly improve the runtime. So, we
can discuss it and I can start working on it.


On Fri, Feb 28, 2014 at 11:15 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

> I'm wondering, with something that is as broadly applicable as pairwise
> alignment, would it be better to implement only in Python (or implement in
> Python wedded to a C backend)?  Or maybe set up something in python that
> taps into an already well-defined C/C++ library that does this?
>
> The reason I mention this: with bioperl we went down this route with
> bioperl-ext a long time ago (these are generally C-based backend tools with
> a perl front-end), that bit-rotted simply b/c there were other more
> maintainable options.  IIUC from this post, similar issues re:
> maintainability held for Bio/pairwise2.py (unless I'm mistaken, which is
> entirely possible).  However, tools like pysam and Bio::DB::Samtools (on
> the perl end) seem to have been maintained much more readily since they tap
> into a common library.
>
> For instance, my suggestion would be to implement a Biopython tool that
> does pairwise alignment using library X (SeqAn, EMBOSS, etc).  Or maybe a
> generic python front-end that allows users to pick the tool/method for the
> alignment, with maybe a library binding as an initial implementation.
>
> chris
>
> On Feb 28, 2014, at 4:07 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>
> > Hi Harsh Beria,
> >
> > One option is to work on pairwise sequence alignments. Currently there
> is some code for that in Biopython (in Bio/pairwise2.py), but it is not
> general and is not being maintained. This may need to be rebuilt from the
> ground up.
> >
> > Best,
> > -Michiel.
> >
> > --------------------------------------------
> > On Wed, 2/26/14, Harsh Beria <harsh.beria93 at gmail.com> wrote:
> >
> > Subject: [Biopython-dev] Gsoc 2014 aspirant
> > To: biopython at lists.open-bio.org, biopython-dev at lists.open-bio.org,
> gsoc at lists.open-bio.org
> > Date: Wednesday, February 26, 2014, 11:14 AM
> >
> > Hi,
> >
> > I am a Harsh Beria, third year UG student at Indian
> > Institute of
> > Technology, Kharagpur. I have started working in
> > Computational Biophysics
> > recently, having written code for pdb to fasta parser,
> > sequence alignment
> > using Needleman Wunch and Smith Waterman, Secondary
> > Structure prediction,
> > Henikoff's weight and am currently working on Monte Carlo
> > simulation.
> > Overall, I have started to like this field and want to carry
> > my interest
> > forward by pursuing a relevant project for GSOC 2014. I
> > mainly code in C
> > and python and would like to start contributing to the
> > Biopython library. I
> > started going through the official contribution wiki page (
> > http://biopython.org/wiki/Contributing)
> >
> > I also went through the wiki page of Bio.SeqlO's. I
> > seriously want to
> > contribute to the Biopython library through GSOC. What do I
> > do next ?
> >
> > Thanks
> > --
> >
> > Harsh Beria,
> > Indian Institute of Technology,Kharagpur
> > <http://www.iitkgp.ac.in/>E-mail: harsh.beria93 at gmail.com
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
> >
> > _______________________________________________
> > Biopython-dev mailing list
> > Biopython-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
>
>


-- 

Harsh Beria,
Indian Institute of Technology,Kharagpur
<http://www.iitkgp.ac.in/>E-mail: harsh.beria93 at gmail.com

Ph: +919332157616