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Título: Local DNA sequence alignment in a cluster of workstations : algorithms and tools
Autor(es): Melo, Alba Cristina Magalhães Alves de
Walter, Maria Emília Machado Telles
Melo, Renata Cristina Faray
Santana, Marcelo Nardelli Pinto
Batista, Rodolfo Bezerra
Assunto: Algoritmos genéticos
Bioengenharia - Ciência da computação
DNA
Data de publicação: Nov-2004
Editora: Sociedade Brasileira de Computação - UFRGS
Referência: MELO, Alba Cristina M. A. et al. Local DNA sequence alignment in a cluster of workstations: algorithms and tools. Journal of the Brazilian Computer Society, Campinas, v. 10, n.2, p.73-80, nov., 2004. Disponível em: <http://www.scielo.br/pdf/jbcos/v10n2/06.pdf>. Acesso em: 28 fev. 2013. http://dx.doi.org/10.1007/BF03192360
Resumo: Distributed Shared Memory systems allow the use of the shared memory programming paradigm in distributed architectures where no physically shared memory exist. Scope consistent software DSMs provide a relaxed memory model that reduces the coherence overhead by ensuring consistency only at synchronization operations, on a per-lock basis. Much of the work in DSM systems is validated by benchmarks and there are only a few examples of real parallel applications running on DSM systems. Sequence comparison is a basic operation in DNA sequencing projects, and most of sequence comparison methods used are based on heuristics, that are faster but do not produce optimal alignments. Recently, many organisms had their DNA entirely sequenced, and this reality presents the need for comparing long DNA sequences, which is a challenging task due to its high demands for computational power and memory. In this article, we present and evaluate a parallelization strategy for implementing a sequence alignment algorithm for long sequences. This strategy was implemented in JIAJIA, a scope consistent software DSM system. Our results on an eight-machine cluster presented good speedups, showing that our parallelization strategy and programming support were appropriate.
Licença: Journal of the Brazilian Computer Society - Esta obra está licenciada sob uma Licença Creative Commons ( Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)). Fonte: http://www.scielo.br/scielo.php?pid=S0104-65002004000300006&script=sci_arttext. Acesso em: 28 fev. 2013.
DOI: http://dx.doi.org/10.1007/BF03192360
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