Accelerating Computation of DNA Sequence Alignment in Distributed Environment

  • Tao Guo
  • Guiyang Li
  • Russel Deaton
Part of the Communications in Computer and Information Science book series (CCIS, volume 15)


Sequence similarity and alignment are most important operations in computational biology. However, analyzing large sets of DNA sequence seems to be impractical on a regular PC. Using multiple threads with JavaParty mechanism, this project has successfully implemented in extending the capabilities of regular Java to a distributed environment for simulation of DNA computation. With the aid of JavaParty and the design of multiple threads, the results of this study demonstrated that the modified regular Java program could perform parallel computing without using RMI or socket communication. In this paper, an efficient method for modeling and comparing DNA sequences with dynamic programming and JavaParty was firstly proposed. Additionally, results of this method in distributed environment have been discussed.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Tao Guo
    • 1
  • Guiyang Li
    • 1
  • Russel Deaton
    • 2
  1. 1.College of Computer ScienceSichuan Normal UniversityChengduChina
  2. 2.College of Computer Science and EngineeringUniversity of ArkansasFayettevilleUSA

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