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

fYear

2014

fDate

13-15 Oct. 2014

Firstpage

282

Lastpage

285

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;

fLanguage

English

Publisher

ieee

Conference_Titel

Cyber-Enabled Distributed Computing and Knowledge Discovery (CyberC), 2014 International Conference on

Conference_Location

Shanghai

Print_ISBN

978-1-4799-6235-8

Type

conf

DOI

10.1109/CyberC.2014.57

Filename

6984320