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

TL;DR

This paper introduces SwissAlign, a webserver that enables fast and exact sequence alignment using the Smith-Waterman algorithm, achieving speeds comparable to heuristic methods like BLAST.

Contribution

It presents a novel technique combining database preprocessing and CPU-specific coding to significantly speed up the Smith-Waterman algorithm.

Findings

Exact Smith-Waterman results are more accurate than BLAST.

SwissAlign achieves near-BLAST speed with exact alignment.

The webserver is publicly available at the specified URL.

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.