Hello - I have added another tutorial to the Biojava in anger pages. This one explains how to generate a pair-wise alignment between two sequences. The solution also demonstrates a lot of how HMMs work in biojava. You can find it under the Weight Matrix and Dynamic Programming section.
http://www.biojava.org/docs/bj_in_anger/ http://www.biojava.org/docs/bj_in_anger/PairAlign.htm Enjoy! Mark Schreiber Principal Scientist (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
