A parallel GPU-designed algorithm for the constrained multiple sequence alignment problem

Abstract

Modern graphical processing units (GPUs) offer much more computational power than modern CPUs, so it is natural that GPUs are often used for solving many computationally-intensive problems. One of the tasks of huge importance in bioinformatics is sequence alignment. We investigate its variant introduced a few years ago in which some additional requirement on the alignment is given. As a result we propose a parallel version of Center-Star algorithm computing the constrained multiple sequence alignment at the GPU. The obtained speedup over the serial CPU relative is in range [20, 200]. © 2011 Springer-Verlag Berlin Heidelberg.