[GSoC] BioJava- Porting the BLAST,HMMER algorithms

[Andreas Prlic]

Hi Ruchin,

Are you also on the biojava-l mailing list? We had quite a number of
discussions about this project already there and if you are not on the
list it might be a good start to catch up with what was already
discussed there.

http://lists.open-bio.org/pipermail/biojava-l/

The idea in short is to come up with an all-Java version of some of
the frequently used algorithms. We are quite flexible regarding the
projects and what we are really
looking for are sound projects  and motivated students. What is
expected is a realistic project proposal, which in turn depends on
your background and how you propose to conduct the project.

Andreas

On Sun, Apr 1, 2012 at 4:23 AM, Ruchin Shah <shahruchin711 at gmail.com> wrote:
> Hi,
>
> I am Ruchin Shah, 3rd year undergraduate student from DA-IICT,India.
>
>         I would like to work on some challenging projects in the field of
> bioinformatics. I have already worked on a project called
> BioSpectroGram(written in Java)under the mentorship of Prof. Manish K.
> Gupta(http://www.guptalab.org/mankg/public_html/) which aims at analyzing
> DNA and protein sequences using various kinds of
> transfromations(FFT,DCT,etc.). I came to know about the idea of implementing
> the two algorithms-BLAST and HMMER, and i find it very fascinating. I have
> a good coding experience(http://www.spoj.pl/users/ruchinshah/). I am also
> familiar with the FASTA and GenBank formats.
>
>         I read about the BLASTA algorithm at
> http://en.wikipedia.org/wiki/BLAST#BLAST but if possible I would like to
> know more about these two algorithms and exactly what is expected from the
> project
> and also some more references.If I am not wrong then you are expecting to
> use some C-to-Java conversion tool or JNI to exploit the already available
> BLAST+ tool and not implement the algorithms from scratch .
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