Fast and Exact Sequence Alignment with the Smith-Waterman Algorithm: The SwissAlign Webserver

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.