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The Potential of Intel Xeon Phi for DNA Sequence Analysis
Linnaeus University, Faculty of Technology, Department of Computer Science. (Parallel Computing)
Linnaeus University, Faculty of Technology, Department of Computer Science. (Parallel Computing)
2015 (English)In: ACACES 2015: Advanced Computer Architecture and Compilation for High-Performance and Embedded Systems, 2015, 263-266 p.Conference paper, Poster (Other academic)
Abstract [en]

Genetic information is increasing exponentially, doubling every 18 months. Analyzing this information within a reasonable amount of time requires parallel computing resources. While considerable research has addressed DNA analysis using GPUs, so far not much attention has been paid to the Intel Xeon Phi coprocessor. In this paper we present an algorithm for large-scale DNA analysis that exploits the thread-level and the SIMD parallelism of the Intel Xeon Phi coprocessor. We evaluate our approach for various numbers of cores and thread allocation affinities in the context of real-world DNA sequences of mouse, cat, dog, chicken, human and turkey. The experimental results on Intel Xeon Phi show speed-ups of up to 10× compared to a sequential implementation running on an Intel Xeon processor E5.

Place, publisher, year, edition, pages
2015. 263-266 p.
Keyword [en]
DNA Analysis, Intel Xeon Phi, Many-core, Pattern Matching, k-mers
National Category
Computer Systems
Research subject
Computer and Information Sciences Computer Science, Computer Science
URN: urn:nbn:se:lnu:diva-45880ISBN: 978-88-905806-3-5OAI: diva2:848866
Available from: 2015-08-26 Created: 2015-08-26 Last updated: 2015-08-26Bibliographically approved

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Memeti, SuejbPllana, Sabri
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