The Smith-Waterman Tool

Smith-Waterman (SW) searching method compares the query to each sequence in database using the full Smith-Waterman algorithm for pairwise comparisons [6]. It also uses search results to generate statistics. Since SW searching is exhaustive, it is the slowest method. We use a special hardware + software (Bioccelerator) to accelerate the application. A Bioccelerator can be found in the TAV bio-informatics department. Direct pointer: [10]
It also can be run through the Weizmann Institute site: [7]