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Applying SIMD Approach to Whole Genome Comparison on Commodity Hardware

  • Conference paper
Parallel Processing and Applied Mathematics (PPAM 2007)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4967))

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Abstract

Whole genome comparison compares (aligns) two genome sequences assuming that analogous characteristics may be found. In this paper, we present an SIMD version of the Smith-Waterman algorithm utilizing Streaming SIMD Extensions (SSE), running on Intel Pentium processors. We compare two approaches, one requiring explicit data dependency handling and one built to automatically handle dependencies and establish their optimal performance conditions.

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Roman Wyrzykowski Jack Dongarra Konrad Karczewski Jerzy Wasniewski

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© 2008 Springer-Verlag Berlin Heidelberg

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Jacob, A., Paprzycki, M., Ganzha, M., Sanyal, S. (2008). Applying SIMD Approach to Whole Genome Comparison on Commodity Hardware. In: Wyrzykowski, R., Dongarra, J., Karczewski, K., Wasniewski, J. (eds) Parallel Processing and Applied Mathematics. PPAM 2007. Lecture Notes in Computer Science, vol 4967. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68111-3_129

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  • DOI: https://doi.org/10.1007/978-3-540-68111-3_129

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-68105-2

  • Online ISBN: 978-3-540-68111-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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