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

fYear

2014

fDate

24-27 Sept. 2014

Firstpage

151

Lastpage

157

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;

fLanguage

English

Publisher

ieee

Conference_Titel

Advances in Computing, Communications and Informatics (ICACCI, 2014 International Conference on

Conference_Location

New Delhi

Print_ISBN

978-1-4799-3078-4

Type

conf

DOI

10.1109/ICACCI.2014.6968196

Filename

6968196