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Agung Widyo Utomo
Bogor Agricultural University

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Parallelization of Pairwise Alignment and Neighbor-Joining Algorithm in Progressive Multiple Sequence Alignment Agung Widyo Utomo
Indonesian Journal of Electrical Engineering and Computer Science Vol 9, No 1: January 2018
Publisher : Institute of Advanced Engineering and Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11591/ijeecs.v9.i1.pp234-242

Abstract

Progressive multiple sequence alignment ClustalW is a widely used heuristic method for computing multiple sequence alignment (MSA). It has three stages: distance matrix computation using pairwise alignment, guide tree reconstruction using neighbor-joining and progressive alignment. To accelerate computing for large data, the progressive MSA algorithm needs to be parallelized. This research aims to identify, decompose and implement the pairwise alignment and neighbor-joining in progressive MSA using message passing, shared memory and hybrid programming model in the computer cluster. The experimental results obtained shared memory programming model as the best scenario implementation with speed up up to 12 times.
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