Hybrid aligment is a variant of the Smith-Waterman algorithm for similarity detection between biological sequences. The advantage of hybrid alignment over the Smith-Waterman algorithm is that the statistics of hybrid alignments are much better characterized than for the Smith-Waterman algorithm. In order to report a p-value for a Smith-Waterman alignment large simulations are necessary. This server calculates p-values for hybrid alignments with arbitrary scoring matrices and gap costs in realtime. A modified version of the BLAST program that utilizes hybrid alignments instead of Smith-Waterman alignments is available to academic users upon request.
If you want to know more about what hybrid alignment is,
please read the articles
Yi-Kuo Yu and Terence Hwa, Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden Markov Models, J. Comp. Biol. 8 (2001), 249-282
Yi-Kuo Yu, Ralf Bundschuh, and Terence Hwa, Hybrid Alignment: High Performance with Universal Statistics, Bioinformatics 18, 864-872 (2002).
For questions and/or comments please send an email to firstname.lastname@example.org.