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

fYear

1995

fDate

25-28 Apr 1995

Firstpage

190

Lastpage

195

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;

fLanguage

English

Publisher

ieee

Conference_Titel

Parallel Processing Symposium, 1995. Proceedings., 9th International

Conference_Location

Santa Barbara, CA

Print_ISBN

0-8186-7074-6

Type

conf

DOI

10.1109/IPPS.1995.395931

Filename

395931