A parallel algorithm for DNA sequences alignment based on MPI

Author

Qianfei Xue ; Jiang Xie ; Junhui Shu ; Huiran Zhang ; Dongbo Dai ; Xing Wu ; Wu Zhang

Author_Institution

High Performance Comput. Center, Shanghai Univ., Shanghai, China

Volume

2

fYear

2014

fDate

26-28 April 2014

Firstpage

786

Lastpage

789

Abstract

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 applying 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

DNA; application program interfaces; bioinformatics; genomics; message passing; molecular biophysics; parallel algorithms; DNA sequence alignment; FED algorithm; MPI; biology research; message passing interface; parallel algorithm; Abstracts; DNA; Encoding; Parallel algorithms; Silicon; MPI; encoded DNA sequences; parallel algorithms; sequences alignment;

fLanguage

English

Publisher

ieee

Conference_Titel

Information Science, Electronics and Electrical Engineering (ISEEE), 2014 International Conference on

Conference_Location

Sapporo

Print_ISBN

978-1-4799-3196-5

Type

conf

DOI

10.1109/InfoSEEE.2014.6947774

Filename

6947774