Sequence Comparison on a Cluster of Workstations Using the PVM System

Sequence comparison is one of the most important tools in molecular biology research. As the amount of DNA data increases rapidly, efficient sequence comparison algorithms are essential in studying newly discovered sequences. We have implemented a distributed sequece comparison algorithm by Smith and Waterman on a cluster of workstations using the PVM paradigm. This implementation has achieved similar performance to the Intel iPSC/860 Hypercube, a massively parallel computer. The distributed Smith-Waterman algorithm serves as a search tool for two Internet algorithm serves GRAIL and GENQUEST. This paper describes the implementation and the performance of the algorithm.