TITLE:
Improvements in the score matrix calculation method using parallel score estimating algorithm
AUTHORS:
Geraldo F. D. Zafalon, Evandro A. Marucci, Julio C. Momente, José R. A. Amazonas, Liria M. Sato, José M. Machado
KEYWORDS:
Algorithms; Scoring Matrix; Parallel Programming; Alignment Quality
JOURNAL NAME:
Journal of Biophysical Chemistry,
Vol.4 No.2,
May
24,
2013
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.