Title :
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
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;
Conference_Titel :
Information Science, Electronics and Electrical Engineering (ISEEE), 2014 International Conference on
Conference_Location :
Sapporo
Print_ISBN :
978-1-4799-3196-5
DOI :
10.1109/InfoSEEE.2014.6947774
