International Journal of Computers


ISSN: 1998-4308
Volume 12, 2018

Notice: As of 2014 and for the forthcoming years, the publication frequency/periodicity of NAUN Journals is adapted to the 'continuously updated' model. What this means is that instead of being separated into issues, new papers will be added on a continuous basis, allowing a more regular flow and shorter publication times. The papers will appear in reverse order, therefore the most recent one will be on top.

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Volume 12, 2018


Title of the Paper: Massively Parallel Multiple Sequence Alignment on the Supercomputer JUQUEEN

 

Authors: Plamenka Borovska, Veska Gancheva

Pages: 1-8

Abstract: In silico biological sequence processing is a key task in molecular biology. This scientific area requires powerful computing resources for exploring large sets of biological data. Parallel in silico simulations based on methods and algorithms for analysis of biological data using high-performance distributed computing is essential for accelerating the research and reducing the investment. Multiple sequence alignment is a widely used method for biological sequence processing. The paper focuses on performance investigation and improvement of multiple biological sequence alignment software MSA_BG on the BlueGene/Q supercomputer JUQUEEN. Experimental simulations on the basis of parallel implementation of MSA_BG algorithm for multiple sequences alignment have been carried out for the case study of the influenza virus variability investigation. The objectives of the investigation are code optimization, porting, scaling, profiling and performance evaluation of MSA_BG software. A hybrid MPI/OpenMP parallelization has been developed and the advantages of this approach through the results of benchmark tests, performed on JUQUEEN have been shown. The experimental results show that the hybrid parallel implementation provides considerably better performance than the MPI only implementation.