Improvements in the score matrix calculation method using parallel score estimating algorithm

Geraldo F. D. Zafalon, Evandro A. Marucci, Julio C. Momente, José R. A. Amazonas, Liria M. Sato, José M. Machado

Departamento de Ciências de Computa??o e Estatística, S?o Paulo State University Rua Cristóv?o Colombo, S?o José do Rio Preto, S?o Paulo, Brazil.
Escola Politécnica University of S?o Paulo Av. Prof. Luciano Gualberto, S?o Paulo, Brazil.

DOI: 10.4236/jbpc.2013.42006                

Abstract

The increasing amount of sequences stored in genomic databases has become unfeasible to the sequential analysis. Then, the parallel computing brought its power to the Bioinformatics through parallel algorithms to align and analyze the sequences, providing improvements mainly in the running time of these algorithms. In many situations, the parallel strategy contributes to reducing the computational complexity of the big problems. This work shows some results obtained by an implementation of a parallel score estimating technique for the score matrix calculation stage, which is the first stage of a progressive multiple sequence alignment. The performance and quality of the parallel score estimating are compared with the results of a dynamic programming approach also implemented in parallel. This comparison shows a significant reduction of running time. Moreover, the quality of the final alignment, using the new strategy, is analyzed and compared with the quality of the approach with dynamic programming.

Keywords

Algorithms; Scoring Matrix; Parallel Programming; Alignment Quality

Conflicts of Interest

The authors declare no conflicts of interest.

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