Utilizing MPJ Express Software in Parallel DNA Sequence Alignment

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. A DNA sequence database is replicated on each processor and therefore the processor has read and writes access to its own database. The model has been evaluated over a network of six processors (one master and five workers) and 24,000 real DNA sequences downloaded from the bio-mirror portal have been used in the experiments.