Abstract
It is demonstrated earlier that the exact Smith–Waterman algorithm yields more accurate results than the members of the heuristic BLAST family of algorithms. Unfortunately, the Smith–Waterman algorithm is much slower than the BLAST and its clones. Here we present a technique and a webserver that uses the exact Smith–Waterman algorithm, and it is approximately as fast as the BLAST algorithm. The technique unites earlier methods of extensive preprocessing of the target sequence database, and CPU-specific coding of the Smith–Waterman algorithm. The SwissAlign webserver is available at the http://swissalign.pitgroup.org address.
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