Using a DSM application to locally align DNA sequences

Abstract

Sequence comparison is a basic operation in DNA sequencing projects, and most sequence comparison methods used are based on heuristics, that are faster but do not produce optimal alignments. Recently, many organisms have had their DNA entirely sequenced, and this reality presents the need for comparing long DNA sequences, which is a challenging task due to its high demands for computational power and memory. Although DSM is presented as a feasible parallel programming paradigm, much of the work in DSM is validated by benchmarks and there are only a few examples of real parallel applications running on DSM systems. In this article, we present and evaluate a parallelization strategy for implementing a local DNA sequence alignment algorithm. This strategy was implemented in JIAJIA, a scope consistent software DSM system. Our results on an eight-machine cluster presented very good speedups, which are comparable with the ones obtained with MPI, showing that our parallelization strategy and programming support were appropriate.