期刊
BIOINFORMATICS
卷 26, 期 5, 页码 683-686出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btq017
关键词
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类别
资金
- Ministerio de Ciencia e Innovacion [AGL2006-12550-C02-01, AGL2006-12550-C02-02]
- 'Consejer a de Agricultura y Pesca' of 'Junta de Andalucia' [041/C/2007]
- Grupo PAI [AGR-248]
- 'Universidad de Cordoba' (Ayuda a Grupos), Spain
Motivation: 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.
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