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Scalability analysis of progressive alignment in a multicore
dc.contributor.author | Isaza, Sebastian |
dc.contributor.author | Sánchez Castaño, Friman |
dc.contributor.author | Gaydadjiev, Georgi |
dc.contributor.author | Ramírez Bellido, Alejandro |
dc.contributor.author | Valero Cortés, Mateo |
dc.contributor.other | Universitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors |
dc.date.accessioned | 2010-07-07T10:58:03Z |
dc.date.available | 2010-07-07T10:58:03Z |
dc.date.created | 2010 |
dc.date.issued | 2010 |
dc.identifier.citation | Isaza, 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.uri | http://hdl.handle.net/2117/8047 |
dc.description.abstract | Sequence 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.extent | 6 p. |
dc.language.iso | eng |
dc.publisher | IEEE Press. Institute of Electrical and Electronics Engineers |
dc.subject | Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica |
dc.subject | Àrees temàtiques de la UPC::Informàtica::Sistemes d'informació::Bases de dades |
dc.subject.lcsh | Bioinformatics |
dc.subject.lcsh | Database Management Systems |
dc.subject.lcsh | Software architecture |
dc.title | Scalability analysis of progressive alignment in a multicore |
dc.type | Conference report |
dc.subject.lemac | Bioinformàtica |
dc.subject.lemac | Programari -- Arquitectura |
dc.subject.lemac | Bases de dades -- Gestió |
dc.contributor.group | Universitat Politècnica de Catalunya. CAP - Grup de Computació d'Altes Prestacions |
dc.identifier.doi | 10.1109/CISIS.2010.149 |
dc.description.peerreviewed | Peer Reviewed |
dc.relation.publisherversion | http://ieeexplore.ieee.org/document/5447487/ |
dc.rights.access | Open Access |
local.identifier.drac | 2574186 |
dc.description.version | Postprint (published version) |
local.citation.author | Isaza, S.; Sanchez, F.; Gaydadjiev, G.; Ramirez, A.; Valero, M. |
local.citation.contributor | CISIS |
local.citation.pubplace | Cracovia |
local.citation.publicationName | 2010 International Conference on Complex, Intelligent and Software Intensive Systems |
local.citation.startingPage | 889 |
local.citation.endingPage | 894 |