DNA sequence alignment is the most

commonly application in computational biology. It is

essential pre-requisite of many other operations in

computational biology applications. Optimal alignment

for a large scale size DNA sequence dataset is a known

example of a time and space consuming. The Smith-

Waterman algorithm is a well recognized technique to

produce optimal alignment between DNA sequences. In

this paper, we present a parallel technique for computing

Smith-Waterman algorithm. The implementation is done

under a master-worker based distributed memory

multiprocessors with Single Program Multiple Data

(SPMD) architecture. The MPJ Express, an object

oriented Message Passing Interface software is utilized to

enable instructions and messages to be exchanged

between processors.