Next-generation bioinformatics: Using many-core processor architecture to develop a web service for sequence alignment
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. 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.
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | artículo biblioteca |
| Language: | Spanish / Castilian |
| Published: |
Oxford University Press
2010-01-16
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| Online Access: | http://hdl.handle.net/10261/90166 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/501100011011 |
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| Summary: | 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. 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. |
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