Applying SIMD Approach to Whole Genome Comparison on Commodity Hardware

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.

• Type: Conference
• Year: 2007
• Where: PPAM
• Authors: Arpith C. Jacob, Marcin Paprzycki, Maria Ganzha, Sugata Sanyal
• Keywords: Intel Pentium Processors, Mathematics, PPAM 2007, Streaming SIMD Extensions, Whole Genome Comparison