On Tue, Dec 05, 2006 at 01:33:56PM +0100, Robert Goldwein <robert.goldwein@dtptools.com> wrote:
Hello all,
for my thesis, I'll be developing a self-contained framework for algorithms used in bioinformatics. This will include algorithms such as Hamming distance, Levenshtein distance or Longest common subsequence algorithms, gene prediction algorithms, 2D and 3D scoring matrices, alignment problems, etc.
I once worked for the bioinfotmatics department in Würzburg. I boostfied (spirit based parsers) profdist http://www.biozentrum.uni-wuerzburg.de/profdist.html and cbcanalyzer http://www.biozentrum.uni-wuerzburg.de/cbcanalyzer.html Before I left I was working on more stable sequence distance correction algorithms, and more generic datastructures to represent plain sequence information and sequence files with structure information. In general I think you should also look for algorithms used in statistic methods. Regards Andreas Pokorny