Advances in GPU Research and Practice

Chapter 8

GPU alignment of two and three sequences

J. Li; S. Ranka; S. Sahni    University of Florida, Gainesville, FL, United States

Abstract

In this chapter, we consider the optimal alignment of two and three sequences using graphics processing units. The problem of aligning two sequences is commonly referred to as pairwise alignment. Experimental results on the NVIDIA Tesla C2050 are presented.

Keywords

GPU; CUDA; Bioinformatics; Performance analysis; Sequence alignment

1 Introduction

1.1 Pairwise alignment

Sequence alignment is a fundamental bioinformatics problem. Algorithms for both pairwise alignment (ie, the alignment of two sequences) and the alignment of three sequences have been intensely researched deeply. In pairwise sequence ...