Efficient Parallel Implementations of Multiple Sequence Alignment using BSP/CGM Model

Authors:
Jucele F. A. Vasconcellos;Christiane Nishibe;Nalvo F. Almeida;Edson N. Cáceres
Affiliations:
College of Computing, UFMS, Campo Grande, Brazil;College of Computing, UFMS, Campo Grande, Brazil;College of Computing, UFMS, Campo Grande, Brazil;College of Computing, UFMS, Campo Grande, Brazil
Venue:
Proceedings of Programming Models and Applications on Multicores and Manycores
Year:
2014

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Abstract

Multiple sequence alignment is a fundamental tool in bioinformatics, widely used for predicting protein structure and function, reconstructing phylogeny and several other biological sequence analyses. Because it is a NP-hard problem, several studies have been conducted to propose efficient methods to solve it. Based on the well-known approximate algorithm proposed by Gusfield [8], we present two parallel solutions for this problem using the BSP/CGM model, with MPI and CUDA implementations. The results show that the use of parallel processing allows the manipulation of more and larger sequences.