Journal Article

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

Sergio Gálvez, David Díaz, Pilar Hernández, Francisco J. Esteban, Juan A. Caballero and Gabriel Dorado

in Bioinformatics

Volume 26, issue 5, pages 683-686
Published in print March 2010 | ISSN: 1367-4803
Published online January 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq017
Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment

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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.

Journal Article.  2236 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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