Accelerating DNA Sequence Analysis using Intel Xeon Phi

TL;DR

This paper presents a parallel DNA analysis algorithm optimized for Intel Xeon Phi, achieving significant speed-ups over traditional CPUs by exploiting thread-level and SIMD parallelism.

Contribution

It introduces a novel DNA analysis algorithm specifically designed for the Intel Xeon Phi coprocessor, leveraging its parallel capabilities.

Findings

Up to 10x speed-up compared to sequential CPU implementation.

Effective utilization of thread-level and SIMD parallelism.

Validated on real-world DNA sequences from multiple species.

Abstract

Genetic information is increasing exponentially, doubling every 18 months. Analyzing this information within a reasonable amount of time requires parallel computing resources. While considerable research has addressed DNA analysis using GPUs, so far not much attention has been paid to the Intel Xeon Phi coprocessor. In this paper we present an algorithm for large-scale DNA analysis that exploits thread-level and the SIMD parallelism of the Intel Xeon Phi. We evaluate our approach for various numbers of cores and thread allocation affinities in the context of real-world DNA sequences of mouse, cat, dog, chicken, human and turkey. The experimental results on Intel Xeon Phi show speed-ups of up to 10x compared to a sequential implementation running on an Intel Xeon processor E5.