[Biopython-dev] [GSoC2013] Codon alignment and analysis in Biopython

[Saket Choudhary]

Hi All,


I am a Fourth Year Undergraduate studying Chemical Engineering at IIT
Bombay, India.

As a warmup, I have been working upon NGS analysis this sem. Besides
playing around with NGS pipelines, scripting one on my own, I have
lately been plying around with the PSSM approach for BWA .
https://github.com/pkerpedjiev/bwa-pssm/  .  So far my contributions
to this project have been only at testing level, I havent really
contributed to the code as such, just reported some bugs.


I have been using BioPython for my Computational Biology Course that I
am doing this semester. I have also been using BIoPython for NGS
analysis, modifying fastq formats and all. I recently contributed to
the BWA wrapper for BioPython
(https://github.com/biopython/biopython/pull/167). I am also working
on the samtools wrapper.


I was a Google Summer of Code 2012 Student for
Connexions(http://cnx.org) and contributed towards SlideImporter
Module(Pyramid/Python): That allows the user to upload SlideShows to
SlideShare and Google Drive and makes a CNXML module out of it.
(https://github.com/oerpub/oerpub.rhaptoslabs.slideimporter). I am
still working for the same organisation and contribute regularly
(https://github.com/oerpub/oerpub.rhaptoslabs.swordpushweb/, Checkout
branches starting with 'saket')

I have deep interest in Biology and have done Molecular and Cell
Biology and the computational aspects of it. BioPython is like the
Best amalgamation for me : Bio + Python



I would like to participate in GSoC 2013 as a student . I would like
to contribute to " Codon Alignment" . Having worked on bwa-pssm
codebase for a while has made me acquainted with alignment algorithms
and I think I can contribute to this.


I have written the first draft of my proposal at
https://docs.google.com/document/d/1xlRSJ74POxi51xn7Web08ACZt4r7KSFIrzRAawTL2ds/edit#heading=h.j7p6z4a3ssy3


Being a first draft it may have  a lot of ambiguity , say I would be
trying to implement a function that is already existing in Biopython
or I would have misinterpreted the problem completely. You can post
your comments on the doc itself and I will try to improve upon it.

Thanks

Saket
https://github.com/saketkc