Title :
Motif Recognition Parallel Algorithm Based on GPU
Author :
Jinliang Zheng ; Jun Lu ; Xinyi Shi ; Yan Shi ; Ruiqing Jing
Author_Institution :
Coll. of Comput. Sci. & Technol., Heilongjiang Univ., Harbin, China
Abstract :
In this paper, a GPU-based parallel algorithm is proposed to improve the processing efficiency of motif recognition algorithm. The work includes a serial motif recognition algorithm and a parallel algorithm based on GPU. Our GPU parallel algorithm is compared with the serial algorithm by using of 1 KB promoter data of five kinds of plant genes upstream regions. The experimental results show that a factor of 20 speeds can be achieved. It means that there are a lot of advantages by GPU parallel technology on gene motif recognition algorithm. It is significant to the great amount of data analysis work of genetic sequence.
Keywords :
bioinformatics; data analysis; genetics; graphics processing units; parallel algorithms; GPU-based parallel algorithm; data analysis; gene motif recognition; genetic sequence; Algorithm design and analysis; Bioinformatics; Biology; Graphics processing units; Instruction sets; Parallel algorithms; Synchronization; GPU parallel; Motif Recognition; Promoter;
Conference_Titel :
Cyber-Enabled Distributed Computing and Knowledge Discovery (CyberC), 2014 International Conference on
Conference_Location :
Shanghai
Print_ISBN :
978-1-4799-6235-8
DOI :
10.1109/CyberC.2014.57
