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A Parallel Algorithm for DNA Sequences Alignment Based on MPI
Xue Qianfei,Xie Jiang * #,Shu Junhui,Zhang Huiran,Dai Dongbo,Wu Xing,Zhang Wu
Schooo of Computer Engineering and Science, Shanghai University, Shanghai 200444
*Correspondence author
#Submitted by
Subject:
Funding: the Specialized Research Fund for the Doctoral Program of Higher Education (No.SRFDP 20113108120022), the Key Project of Science and Technology Commission of Shanghai Municipality (No.No. 11510500300), the Major Research Plan of NSFC (No.No. 91330116)
Opened online:31 March 2014
Accepted by: none
Citation: Xue Qianfei,Xie Jiang,Shu Junhui.A Parallel Algorithm for DNA Sequences Alignment Based on MPI[OL]. [31 March 2014] http://en.paper.edu.cn/en_releasepaper/content/4591143
 
 
DNA sequences have the fundamental information for each species and a comparison between DNA sequences is one of the basic biological problems. There are a large number of algorithms applied in sequence alignment. Some are for approximate alignment, and others are for exact alignment, which also plays an important role in biology research. In this paper, a new parallel algorithm based on FED algorithm for exact sequences alignment with MPI is proposed. The experimental results indicate that the proposed algorithm can report the matched positions in the specific sequence and improve the matching speed with MPI, as well as reduce the storage requirement.
Keywords:encoded DNA sequences; sequences alignment; parallel algorithms; MPI
 
 
 

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