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Título

Next-generation bioinformatics: Using many-core processor architecture to develop a web service for sequence alignment

AutorGálvez, Sergio; Díaz, David ; Hernández Molina, Pilar ; Esteban, Francisco J.; Caballero, Juan Antonio; Dorado, Gabriel
Fecha de publicación16-ene-2010
EditorOxford University Press
CitaciónBioinformatics 26(5): 683-686 (2010)
ResumenMotivation: Bioinformatics algorithms and computing power are the main bottlenecks for analyzing huge amount of data generated by the current technologies, such as the 'next-generation' sequencing methodologies. At the same time, most powerful microprocessors are based on many-core chips, yet most applications cannot exploit such power, requiring parallelized algorithms. As an example of next-generation bioinformatics, we have developed from scratch a new parallelization of the Needleman-Wunsch (NW) sequence alignment algorithm for the 64-core Tile64 microprocessor. The unprecedented performance it offers for a standalone personal computer (PC) is discussed, optimally aligning sequences up to 20 times faster than the non-parallelized version, thus saving valuable time. Availability: This algorithm is available as a free web service for the scientific community at http://www.sicuma.uma.es/multicore. The open source code is also available on such site. Contact: galvez@uma.es Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2010. Published by Oxford University Press.
URIhttp://hdl.handle.net/10261/90166
DOI10.1093/bioinformatics/btq017
Identificadoresdoi: 10.1093/bioinformatics/btq017
issn: 1367-4803
e-issn: 1460-2059
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