[GSoC] BioJava- Porting the BLAST,HMMER algorithms

[Ruchin Shah]

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 .