publication . Master thesis . 2015

Protein Alignment on the Intel Xeon Phi Coprocessor

Ramstad, Jorun;
Open Access English
  • Published: 01 Jan 2015
Abstract
There is an increasing need for sensitive, high perfomance sequence alignemnet tools. With the growing databases of scientificly analyzed protein sequences, more compute power is necessary. Specialized architectures arise, and a transition from serial to specialized implementationsis is required. This thesis is a study of whether Intel 60's cores Xeon Phi coprocessor is a suitable architecture for implementation of a sequence alignment tool. The performance relative to existing tools are evaluated, as well as measurements comparing the implementation to the theoretical peak performance of the architecture. SWIMIC, a sequence alignment tool utilizing the Smith-Wa...
Subjects
free text keywords: Programming, optimaization, bioinformatics, protein, alignment, Xeon, Phi

1 Introduction 1 1.1 Motivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Goal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.3 Tools for Comparison . . . . . . . . . . . . . . . . . . . . . . . . 2 1.4 Overview of Thesis . . . . . . . . . . . . . . . . . . . . . . . . . 2

2 Background 5 2.1 Sequence Alignment . . . . . . . . . . . . . . . . . . . . . . . . 5 2.1.1 Alignment Types . . . . . . . . . . . . . . . . . . . . . . 5 2.1.2 Databases . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2.1.3 Input Format . . . . . . . . . . . . . . . . . . . . . . . . 8 2.2 The Intel Xeon Phi Coprocessor . . . . . . . . . . . . . . . . . . 8 2.2.1 Technical specifications . . . . . . . . . . . . . . . . . . 8 2.2.2 Compilation . . . . . . . . . . . . . . . . . . . . . . . . . 12 2.2.3 Gaining Optimal Performance . . . . . . . . . . . . . . 13

3 Methods 15 3.1 Common Approaches for Alignment . . . . . . . . . . . . . . . 15 3.1.1 BLAST . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 3.1.2 Smith-Waterman . . . . . . . . . . . . . . . . . . . . . . 16 3.2 Existing Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 3.3 Optimization Techniques . . . . . . . . . . . . . . . . . . . . . . 20

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