Parallel multiple sequences alignment in SMP cluster

Abstract

Multiple sequences alignment is a fundamental and challenging problem in computational molecular biology. It is commonly used to analyse the DNA/protein sequences. To develop a high efficient parallel algorithm is a very important solution to speedup this time consuming problem. However, due to the irregular computation behaviors based on tree, it is difficult to achieve good load balancing, so the utilization of processor is very low. This paper presents a parallel multiple sequences alignment algorithm featuring a mixed fine and coarse grained parallelization approach. The parallel algorithm is suitable to be implemented in SMP cluster, which is the main architecture of current cluster systems. We implemented the parallel algorithm in SMP cluster using a hybrid MPI/OpenMP method and the experimental results shows that the mixed fine and coarse algorithm achieves higher speedup