Next-generation bioinformatics
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DescriptionUsing many-core processor architecture to develop a web service for sequence alignment
Homepagehttp://www.sicuma.uma.es/multicore
Publications
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; Gabriel Dorado
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.
DOI: https://doi.org/10.1093/bioinformatics/btq017
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