MOTIVATION The only algorithm guaranteed to find the optimal local alignment is the Smith-Waterman. It is also one of the slowest due to the number of computations required for the search. To speed up the algorithm, Single-Instruction Multiple-Data (SIMD) instructions have been used to parallelize the algorithm at the instruction level. RESULTS A faster implementation of the Smith-Waterman al...

The Smith-Waterman algorithm is a dynamic programming method for determining optimal local alignments between nucleotide or protein sequences. However, it suffers from quadratic time and space complexity. As a result, many algorithmic and architectural enhancements have been proposed to solve this problem, but at the cost of reduced sensitivity in the algorithms or significant expense in hardwa...

Sequence comparison is a basic operation in DNA sequencing projects, and most of sequence comparison methods are based on heuristics, which are fast but not sensitive. The Dynamic Programming Algorithm, Smith-Waterman, obtains the best alignment, but at the expense of computational time. Unfortunately, the inefficiency in the performance of the Smith-Waterman algorithm limits its applications i...

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 SmithWaterman algorithm, and it is approximately as fast as the BLAST algorithm. The ...