Local DNA sequence alignment in a cluster of workstations : algorithms and tools

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MetadadosDescriçãoIdioma
Autor(es): dc.creatorMelo, Alba Cristina Magalhães Alves de-
Autor(es): dc.creatorWalter, Maria Emília Machado Telles-
Autor(es): dc.creatorMelo, Renata Cristina Faray-
Autor(es): dc.creatorSantana, Marcelo Nardelli Pinto-
Autor(es): dc.creatorBatista, Rodolfo Bezerra-
Data de aceite: dc.date.accessioned2021-10-14T18:38:08Z-
Data de disponibilização: dc.date.available2021-10-14T18:38:08Z-
Data de envio: dc.date.issued2013-02-28-
Data de envio: dc.date.issued2013-02-28-
Data de envio: dc.date.issued2004-11-
Fonte completa do material: dc.identifierhttp://repositorio.unb.br/handle/10482/12255-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1007/BF03192360-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/capes/636344-
Descrição: dc.descriptionDistributed 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.-
Formato: dc.formatapplication/pdf-
Publicador: dc.publisherSociedade Brasileira de Computação - UFRGS-
Direitos: dc.rightsAcesso Aberto-
Direitos: dc.rightsJournal 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.-
Palavras-chave: dc.subjectAlgoritmos genéticos-
Palavras-chave: dc.subjectBioengenharia - Ciência da computação-
Palavras-chave: dc.subjectDNA-
Título: dc.titleLocal DNA sequence alignment in a cluster of workstations : algorithms and tools-
Tipo de arquivo: dc.typelivro digital-
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