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dc.contributor.authorIsaza, Sebastian
dc.contributor.authorSánchez Castaño, Friman
dc.contributor.authorGaydadjiev, Georgi
dc.contributor.authorRamírez Bellido, Alejandro
dc.contributor.authorValero Cortés, Mateo
dc.contributor.otherUniversitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors
dc.date.accessioned2010-07-07T10:58:03Z
dc.date.available2010-07-07T10:58:03Z
dc.date.created2010
dc.date.issued2010
dc.identifier.citationIsaza, S. [et al.]. Scalability analysis of progressive alignment in a multicore. A: CISIS. "2010 International Conference on Complex, Intelligent and Software Intensive Systems". Cracovia: IEEE Press. Institute of Electrical and Electronics Engineers, 2010, p. 889-894.
dc.identifier.urihttp://hdl.handle.net/2117/8047
dc.description.abstractSequence alignment is a fundamental instrument in Bioinformatics. In recent years, numerous proposals have been addressing the problem of accelerating this class of applications. This, due to the rapid growth of sequence databases in combination with the high computational demands imposed by the algorithms. In this paper we focus on the analysis of the progressive alignment in ClustalW, a widely used program for performing multiple sequence alignment. We have parallelized ClustalW for the Cell processor architecture and have carefully analyzed the scalability of its different phases with both the number of cores used and the input size. Experimental results show that computing profile scores scales well up to 16 SPE cores. With the increase of the input size, profiles initialization in the PPE core becomes the predominant bottleneck.
dc.format.extent6 p.
dc.language.isoeng
dc.publisherIEEE Press. Institute of Electrical and Electronics Engineers
dc.subjectÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
dc.subjectÀrees temàtiques de la UPC::Informàtica::Sistemes d'informació::Bases de dades
dc.subject.lcshBioinformatics
dc.subject.lcshDatabase Management Systems
dc.subject.lcshSoftware architecture
dc.titleScalability analysis of progressive alignment in a multicore
dc.typeConference report
dc.subject.lemacBioinformàtica
dc.subject.lemacProgramari -- Arquitectura
dc.subject.lemacBases de dades -- Gestió
dc.contributor.groupUniversitat Politècnica de Catalunya. CAP - Grup de Computació d'Altes Prestacions
dc.identifier.doi10.1109/CISIS.2010.149
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttp://ieeexplore.ieee.org/document/5447487/
dc.rights.accessOpen Access
local.identifier.drac2574186
dc.description.versionPostprint (published version)
local.citation.authorIsaza, S.; Sanchez, F.; Gaydadjiev, G.; Ramirez, A.; Valero, M.
local.citation.contributorCISIS
local.citation.pubplaceCracovia
local.citation.publicationName2010 International Conference on Complex, Intelligent and Software Intensive Systems
local.citation.startingPage889
local.citation.endingPage894


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