A way for accelerating DNA sequences reconstruction problem based on CUDA

摘要

Traditionally, shotgun for DNA sequences alignment is one of the main method of bioinformatics. It is used to break a long DNA sequence into small fragments. This paper introduces a new method to improve the efficiency of DNA sequence reconstruction after shotgun method using construction suffix array based on CUDA programming model. The experimental results show the construction of suffix array using GPU is an more efficient approach on Intel(R) Core(TM) i3-3110K quad-core and NVIDIA GeForce 610M GPU. Consequently, The experiment presents the efficiency of GPU performance compared with CPU performance, and study shows the method is more than 20 times speedup than that of CPU serial implementation.