DNA sequence alignment: hybrid parallel programming on a multicore cluster

dc.creatorRucci, Enzo
dc.creatorDe Giusti, Armando Eduardo
dc.creatorChichizola, Franco
dc.creatorNaiouf, Marcelo
dc.creatorDe Giusti, Laura Cristina
dc.date2011-09-15
dc.date2011
dc.date2019-10-15T13:22:01Z
dc.identifierhttp://sedici.unlp.edu.ar/handle/10915/83228
dc.identifierisbn:978-1-61804-030-5
dc.descriptionDNA sequence alignment is one of the most important operations of computational biology. In 1981, Smith and Waterman developed a method for sequences local alignment. Due to its computational power and memory requirements, various heuristics have been developed to reduce execution time at the expense of a loss of accuracy in the result. This is why heuristics do not ensure that the best alignment is found. For this reason, it is interesting to study how to apply the computer power of different parallel platforms to speed up the sequence alignment process without losing result accuracy. In this article, a new parallelization strategy (HI-M) of Smith-Waterman algorithm on a multi-core cluster is presented, configuring a pipeline with a hybrid communication model. Additionally, a performance analysis is carried out and compared with two previously presented parallel solutions. Finally, experimental results are presented, as well as future research lines.
dc.descriptionFacultad de Informática
dc.formatapplication/pdf
dc.languageen
dc.rightshttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
dc.subjectCiencias Informáticas
dc.subjectBioinformatics
dc.subjectSequence alignment
dc.subjectParallel algorithms
dc.subjectMulticore cluster
dc.subjectPipeline computing
dc.titleDNA sequence alignment: hybrid parallel programming on a multicore cluster
dc.typeObjeto de conferencia
dc.typeObjeto de conferencia


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