Title :
Sequence comparison on a cluster of workstations using the PVM system
Author :
Guan, X. ; Mural, R.J. ; Uberbacher, E.C.
Author_Institution :
Div. of Comput. Sci. & Math., Oak Ridge Nat. Lab., TN, USA
Abstract :
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
Keywords :
DNA; Internet; hypercube networks; medical computing; molecular biophysics; DNA data; GENQUEST; Intel iPSC/860 hypercube; Internet servers GRAIL; PVM system; cluster of workstations; massively parallel computer; molecular biology research; performance; sequence comparison; Clustering algorithms; Computer science; Concurrent computing; DNA; Databases; Laboratories; Mathematics; Proteins; Sequences; Workstations;
Conference_Titel :
Parallel Processing Symposium, 1995. Proceedings., 9th International
Conference_Location :
Santa Barbara, CA
Print_ISBN :
0-8186-7074-6
DOI :
10.1109/IPPS.1995.395931
