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High Performance Parallelism Pearls Volume Two by James Reinders, Jim Jeffers

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Chapter 4

Pairwise DNA Sequence Alignment Optimization

Yongchao Liu*; Bertil Schmidt    * Georgia Institute of Technology, USA Johannes Gutenberg University Mainz, Germany

Abstract

This chapter presents a parallel implementation of the Smith-Waterman algorithm to accelerate the pairwise alignment of DNA sequences. This algorithm is especially computationally demanding for long DNA sequences. Parallelization approaches are examined in order to deeply explore the inherent parallelism within Intel Xeon Phi coprocessors. This chapter looks at exploiting instruction-level parallelism within 512-bit single instruction multiple data instructions (vectorization) as well as thread-level parallelism over the many cores (multithreading using OpenMP). ...

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