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. © 2008 Springer-Verlag Berlin Heidelberg.
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CITATION STYLE
Jacob, A., Paprzycki, M., Ganzha, M., & Sanyal, S. (2008). Applying SIMD approach to whole genome comparison on commodity hardware. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 4967 LNCS, pp. 1220–1229). https://doi.org/10.1007/978-3-540-68111-3_129
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