The multiple sequence alignment problem in biology
SIAM Journal on Applied Mathematics
Trees, stars, and multiple biological sequence alignment
SIAM Journal on Applied Mathematics
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Allocating independent tasks to parallel processors: an experimental study
Journal of Parallel and Distributed Computing - Special issue on dynamic load balancing
MPI versus MPI+OpenMP on IBM SP for the NAS benchmarks
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
Scalable Parallel Computing: Technology,Architecture,Programming
Scalable Parallel Computing: Technology,Architecture,Programming
A More Efficient Approximation Scheme for Tree Alignment
SIAM Journal on Computing
Parallel CLUSTAL W for PC clusters
ICCSA'03 Proceedings of the 2003 international conference on Computational science and its applications: PartII
The Journal of Supercomputing
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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.