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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)

Abstract

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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References

  1. 1.
    Russell, D., et al.: DNA Computing: A Review. Fundamental Informatics 30, 23–41 (1997)Google Scholar
  2. 2.
    Pearson, W.R., Lipman, D.J.: Improved Tools for Biological Sequence Comparison. Proc. Natl. Acad. Sci. 85, 2444–2448 (1988)CrossRefGoogle Scholar
  3. 3.
    Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic Local Alignment Search Tool. J. Mol. Biol. 215, 403–410 (1990)Google Scholar
  4. 4.
    Smith, T.F., Waterman, M.S.: Identification of Common Molecular Subsequences. J. Mol. Biol. 147, 195–197 (1981)CrossRefGoogle Scholar
  5. 5.
    Chintalapati, J., Rajendra, R.J.: Accelerating Comparative Genomics Using Parallel Computing. Silico Biology 3, 36 (2003)Google Scholar
  6. 6.
    Philippsen, M.: Data Parallelism in Java. In: Schaefer, J. (ed.) High Performance Computing Systems and Applications, pp. 85–99. Kluwer Academic Publishers, Dordrecht (1998)Google Scholar
  7. 7.
    Philippsen, M., Zenger, M.: JavaParty-Transparent Remote Objects for Java. Practice and Experience 9(11), 1225–1242 (1997)CrossRefGoogle Scholar
  8. 8.
    Bernhard, H.: Transparent Distributed Threads for Java. 5th Internal Workshop on Java for Parallel and Distributed Computing. In: Conjunction with the International Parallel and Distributed Processing Sysposium (IPDPS 2003), NICE, France (2003)Google Scholar
  9. 9.
    Philippsen, M.: Transparent Remote Objects in Java. Practice and Experience 9(11), 1225–1242 (1997)CrossRefGoogle Scholar

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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