본문 바로가기
  • Home

Study on MPI-based parallel sequence similarity search in the LINUX cluster

  • Journal of The Korea Society of Computer and Information
  • Abbr : JKSCI
  • 2006, 11(6), pp.69-78
  • Publisher : The Korean Society Of Computer And Information
  • Research Area : Engineering > Computer Science

홍창범 1 Seungwoo Shin 2 Keun-Joon Park 1 Park, Keun Yong 1 차정호 1 이성훈 1

1질병관리본부
2순천향대학교부속부천병원

Candidate

ABSTRACT

In the field of the bioinformatics, it plays an important role in predicting functional information or structure information to search similar sequence in biological DB. Biological sequences have been increased dramatically since Human Genome Project. At this point, because the searching speed for the similar sequence is highly regarded as the important factor for predicting function or structure, the SMP(Sysmmetric Multi-Processors) computer or cluster is being used in order to improve the performance of searching time. As the method to improve the searching time of BLAST(Basic Local Alighment Search Tool) being used for the similarity sequence search, We suggest the nBLAST algorithm performing on the cluster environment in this paper. As the nBLAST uses the MPI(Message Passing Interface), the parallel library without modifying the existing BLAST source code, to distribute the query to each node and make it performed in parallel, it is possible to easily make BLAST parallel without complicated procedures such as the configuration. In addition, with the experiment performing the nBLAST in the 28 nodes of LINUX cluster, the enhanced performance according to the increase in the number of the nodes has been confirmed.

Citation status

* References for papers published after 2022 are currently being built.