Title :
Solving the longest overlap region problem for noncoding DNA sequences with GPU
Author :
Yukun Zhong ; JianBiao Lin ; Baoqiu Wang ; Chen Tao ; Che Nian ; Xie Wen
Author_Institution :
Comput. Sci. & Eng. Dept., Sichuan Univ., Penshan, China
Abstract :
Early hardware limitations of GPU (lack of synchronization primitives and limited memory caching mechanisms) can make GPU-based computation inefficient. Now Bio-technologies bring more chances to Bioinformatics and Biological Engineering. Our paper introduces a way to solve the longest overlap region of non-coding DNA sequences on using the Compute Unified Device Architecture (CUDA) platform Intel(R) Core(TM) i3-3110m quad-core. Compared to standard CPU implementation, CUDA performance proves the method of the longest overlap region recognition of noncoding DNA is an efficient approach to high-performance bioinformatics applications. Studies show the fact that efficiency of GPU performance is more than 20 times speedup than that of CPU serial implementation. We believe our method gives a cost-efficient solution to the bioinformatics community for solving longest overlap region recognition problem and other related fields.
Keywords :
DNA; bioinformatics; genomics; graphics processing units; molecular biophysics; parallel architectures; CPU serial implementation; GPU performance efficiency; biological engineering; biotechnologies; compute unified device architecture; high-performance bioinformatics applications; longest overlap region problem; noncoding DNA sequences; Arrays; Bioinformatics; DNA; Graphics processing units; Indexes; Instruction sets; Programming; CUDA; DC3; GPUs; LCP; Noncoding DNA; RMQ; suffix array;
Conference_Titel :
Biomedical Engineering and Informatics (BMEI), 2014 7th International Conference on
Conference_Location :
Dalian
Print_ISBN :
978-1-4799-5837-5
DOI :
10.1109/BMEI.2014.7002858
