A parallel Smith-Waterman algorithm based on divide and conquer

Abstract

Biological sequence comparison is an important tool for researchers in molecular biology. There are several algorithms for sequence comparison. The Smith-Waterman algorithm, based on dynamic programming, is one of the most fundamental algorithms in bioinformatics. However, the existing parallel Smith-Waterman algorithm needs large memory space. As the data of biological sequences expand rapidly, the memory requirement of the existing parallel Smith-Waterman algorithm has becoming a critical problem. For resolving this problem, we develop a new parallel Smith-Waterman algorithm using the method of divide and conquer, named PSW-DC. Memory space required in the new parallel algorithm is reduced significantly in comparison with existing ones. A key technique, named the C&E method, is developed for implementation of the new parallel Smith-Waterman algorithm.