Applying SIMD approach to whole genome comparison on commodity hardware

Authors:
Arpith Jacob;Marcin Paprzycki;Maria Ganzha;Sugata Sanyal
Affiliations:
Department of Computer Science and Engineering, Vellore Institute of Technology, Vellore, India;Systems Research Institute, Polish Academy of Sciences, Warsaw, Poland and Computer Science Department, Warsaw Management Academy, Warsaw, Poland;Systems Research Institute, Polish Academy of Sciences, Warsaw, Poland and Department of Administration, Elblag University of Humanities and Economics, Elblag, Poland;School of Technology and Computer Science, Tata Institute of Fundamental Research, Mumbai, India
Venue:
PPAM'07 Proceedings of the 7th international conference on Parallel processing and applied mathematics
Year:
2007

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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.