Sequence comparison on a cluster of workstations using the PVM system
X. Guan, Richard Mural, E.O. Uberbacher · 2002
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 sequence comparison algorithm by T.F. Smith and M. Waterman (1981) 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 servers GRAIL and GENQUEST. This paper describes the implementation and the performance of the algorithm.>