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
and
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 hybparam@bioserv.mps.ohio-state.edu.