[Biojava-dev] Hello and support for FASTA34

[kdoshi at asuragen.com]

Hello Biojava.

My name is Kishore Doshi. I have been programming in Java and C++ for 8+
years now and I just completed my PhD in Molecular Biology at the
University of Texas at Austin. For my PhD work, I developed a software
toolkit in Java for RNA comparative sequence analysis at the Gutell Lab.

As part of my new job, I have just come across the Biojava API and I am
very impressed with the capabilities available. I wish I would have used
it a few years ago when developing my RNA comparative sequence analysis
toolkit. 

I would be interested in lending my time to help Biojava as it continues
to evolve. One area I have noticed I could provide immediate help would
be in support for parsing FASTA search results. The classes
FastaSearchParser and FastaSearchSAXParser appear to support FASTA 3.3;
however, they do not appear to support FASTA 3.4. I have modified
FastaSearchParser and FastaSearchSAXParser to support the tag
modifications in FASTA 3.4 output. I would be interested in contributing
my changes back to the community if possible. Please advise on how I
should move forward.

Thanks
Kishore Doshi, M.S.;Ph.D. | Bioinformatics
Asuragen, Inc. -- A Spin-Off of Ambion
2150 Woodward, Suite 100, Austin TX USA 78744
Tel: 1-512-681-5397 | Fax: 1-512-681-5201