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Parallelization of Multiple Genome Alignment

  • Yiming Li
  • Cheng-Kai Chen
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3726)

Abstract

In this work, we implement a genome alignment system which applies parallelization schemes to the ClustalW algorithm and the interface of database querying. Parallel construction of the distance matrices and parallelization of progressive alignment in the ClustalW algorithm are performed on PC-based Linux cluster with message-passing interface libraries. Achieved experiments show good speedup and significant parallel performance.

Keywords

Multiple Sequence Alignment Parallel Performance Pairwise Alignment Guide Tree Genome Alignment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Yiming Li
    • 1
    • 2
  • Cheng-Kai Chen
    • 2
    • 3
  1. 1.Department of Communication Engineering 
  2. 2.Microelectronics and Information Systems Research Center 
  3. 3.Department of Computer and Information ScienceNational Chiao Tung UniversityHsinchu City, HsinchuTaiwan

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