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ARTIGO_Exact Parallel Alignment.pdf544,69 kBAdobe PDFVisualizar/Abrir
Título: Exact parallel alignment of megabase genomic sequences with tunable work distribution
Autor(es): Boukerche, Azzedine
Batista, Rodolfo Bezerra
Melo, Alba Cristina Magalhães Alves de
Scarel, Felipe Brandt
Souza, Lavir Antonio Bahia Carvalho de
Assunto: Algoritmos genéticos
Biologia computacional
Programação dinâmica
Bioengenharia - Ciência da computação
Data de publicação: 2012
Editora: Publishing With World Scientific
Referência: BOUKERCHE, Azzedine et al. Exact parallel alignment of megabase genomic sequences with tunable work distribution. International Journal of Foundations of Computer Science, Santa Barbara, v. 23, n. 2, p. 407–429, 2012. Disponível em: <http://www.worldscientific.com/doi/pdfplus/10.1142/S0129054112400205>. Acesso em: 27 fev. 2013. DOI: 10.1142/S0129054112400205
Resumo: Sequence Alignment is a basic operation in Bioinformatics that is performed thousands of times, on daily basis. The exact methods for pairwise alignment have quadratic time complexity. For this reason, heuristic methods such as BLAST are widely used. To obtain exact results faster, parallel strategies have been proposed but most of them fail to align huge biological sequences. This happens because not only the quadratic time must be considered but also the space should be reduced. In this paper, we evaluate the performance of Z-align, a parallel exact strategy that runs in user-restricted memory space. Also, we propose and evaluate a tunable work distribution mechanism. The results obtained in two clusters show that two sequences of size 24MBP (Mega Base Pairs) and 23MBP, respectively, were successfully aligned with Z-align. Also, in order to align two 3MBP sequences, a speedup of 34.35 was achieved for 64 processors. The evaluation of our work distribution mechanism shows that the execution times can be sensibly reduced when appropriate parameters are chosen. Finally, when comparing Z-align with BLAST, it is clear that, in many cases, Z-align is able to produce alignments with higher score.
Licença: International Journal of Foundations of Computer Science - Author Rights All articles published on WorldSciNet are protected by the copyright held by World Scientific Publishing Company (or its subsidiaries). You may share the published (printed or electronic) version provided it is for non-commercial use. Electronic version of an article published as International Journal of Foundations of Computer Science, Vol. 23, No. 2, 2012 p.407–429 DOI: 10.1142/S0129054112400205 © copyright World Scientific Publishing Company http://www.worldscientific.com/worldscinet/ijfcs. Fonte: http://www.worldscientific.com/page/authors/author-rights. Acesso em: 27 fev. 2013.
DOI: https://dx.doi.org/10.1142/S0129054112400205
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