Title :
A way for accelerating DNA sequences reconstruction problem based on CUDA
Author :
Yukun Zhong ; JianBiao Lin ; Baoqiu Wang ; Chen Tao ; Xie Wen ; Che Nian
Author_Institution :
Comput. Sci. & Eng. Dept., Sichuan Univ. Jinjiang Coll., Penshan, China
Abstract :
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.
Keywords :
DNA; bioinformatics; graphics processing units; parallel architectures; CUDA programming model; DNA sequence reconstruction; DNA sequences alignment; DNA sequences reconstruction problem; Intel Core i3-3110K quadcore; NVIDIA GeForce 610M GPU; bioinformatics; construction suffix array; long DNA sequence; shotgun method; Arrays; DNA; Graphics processing units; CUDA; DNA sequence reassemble; GPU; radix sort; shotgun method; suffix array; superstring;
Conference_Titel :
Advances in Computing, Communications and Informatics (ICACCI, 2014 International Conference on
Conference_Location :
New Delhi
Print_ISBN :
978-1-4799-3078-4
DOI :
10.1109/ICACCI.2014.6968196
