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 [12]. 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 execute the algorithm.
Direct pointer: [19]
It also can be run through the Weizmann Institute site: [16]