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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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
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