Smith-Waterman Searching

While the dynamic programming algorithm is inherently slow,

it is still the most mathematically rigorous method for
sequence similarity search.

Several optimized versions of this method are available over the

internet.
The EMBL offers a service known as MPsrch for protein similarity
searching in databases: !!!!!! Retired!!!!!!
Web: http://www.ebi.ac.uk/MPsrch/

Paralign is an (8x) accelerated Smith-Waterman method for similarity

searching in databases:

Web: http://www.paralign.org/

Introduction to Bioinformatics
Matthias Sipiczki, Department of Genetics, University of Debrecen
Comments to: lipovy@tigris.unideb.hu