Mostra el registre d'ítem simple
Long DNA sequence comparison on multicore architectures
dc.contributor.author | Sánchez Castaño, Friman |
dc.contributor.author | Cabarcas, Felipe |
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 | 2011-01-07T15:14:07Z |
dc.date.available | 2011-01-07T15:14:07Z |
dc.date.created | 2010 |
dc.date.issued | 2010 |
dc.identifier.citation | Sánchez, F., Cabarcas, F., Ramírez, A., Valero, M. Long DNA sequence comparison on multicore architectures. A: EURO-PAR, International European Conference on Parallel and Distributed Computing. "Euro-Par 2010, Parallel Processing: 16th International Euro-Par Conference: Ischia, Italy, August 31-September 3, 2010: proceedings, part II". Ischia: Springer Verlag, 2010, p. 247-259. |
dc.identifier.uri | http://hdl.handle.net/2117/10925 |
dc.description.abstract | Biological sequence comparison is one of the most important tasks in Bioinformatics. Due to the growth of biological databases, sequence comparison is becoming an important challenge for high performance computing, especially when very long sequences are compared. The Smith-Waterman (SW) algorithm is an exact method based on dynamic programming to quantify local similarity between sequences. The inherent large parallelism of the algorithm makes it ideal for architectures supporting multiple dimensions of parallelism (TLP, DLP and ILP). In this work, we show how long sequences comparison takes advantage of current and future multicore architectures. We analyze two different SW implementations on the CellBE and use simulation tools to study the performance scalability in a multicore architecture. We study the memory organization that delivers the maximum bandwidth with the minimum cost. Our results show that a heterogeneous architecture is an valid alternative to execute challenging bioinformatic workloads. |
dc.format.extent | 13 p. |
dc.language.iso | eng |
dc.publisher | Springer Verlag |
dc.subject | Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors |
dc.subject.lcsh | Computer architecture |
dc.subject.lcsh | Multicore architectures |
dc.title | Long DNA sequence comparison on multicore architectures |
dc.type | Conference report |
dc.subject.lemac | Processament en paral·lel (Ordinadors) -- Arquitectura |
dc.subject.lemac | Bioinformàtica |
dc.subject.lemac | Paral·lelisme (Informàtica) |
dc.contributor.group | Universitat Politècnica de Catalunya. CAP - Grup de Computació d'Altes Prestacions |
dc.identifier.doi | 10.1007/978-3-642-15291-7_24 |
dc.description.peerreviewed | Peer Reviewed |
dc.relation.publisherversion | http://www.springerlink.com/content/8h06256153073pt5/ |
dc.rights.access | Restricted access - publisher's policy |
local.identifier.drac | 4430152 |
dc.description.version | Postprint (published version) |
local.citation.author | Sánchez, F.; Cabarcas, F.; Ramírez, A.; Valero, M. |
local.citation.contributor | EURO-PAR, International European Conference on Parallel and Distributed Computing |
local.citation.pubplace | Ischia |
local.citation.publicationName | Euro-Par 2010, Parallel Processing: 16th International Euro-Par Conference: Ischia, Italy, August 31-September 3, 2010: proceedings, part II |
local.citation.startingPage | 247 |
local.citation.endingPage | 259 |