Memory Efficient Pair-Wise Genome Alignment Algorithm – A Small-Scale Application with Grid Potential

  • Nova Ahmed
  • Yi Pan
  • Art Vandenberg
Conference paper

DOI: 10.1007/978-3-540-30208-7_103

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3251)
Cite this paper as:
Ahmed N., Pan Y., Vandenberg A. (2004) Memory Efficient Pair-Wise Genome Alignment Algorithm – A Small-Scale Application with Grid Potential. In: Jin H., Pan Y., Xiao N., Sun J. (eds) Grid and Cooperative Computing - GCC 2004. GCC 2004. Lecture Notes in Computer Science, vol 3251. Springer, Berlin, Heidelberg

Abstract

Grid middleware infrastructure is a distributed environment suitable for many, typically large-scale, applications. An improved genome sequence alignment algorithm is presented that significantly reduces sequence matching computation time. Yet, very long sequences can still present computation challenges. A small-scale application is implemented on a shared memory system, on a cluster, and the grid-enabled cluster. Experimental results show comparable performance of the grid-enabled version, with scalability for large sequences. The grid offers application management, enables dynamic specification of parameters, and enables a choice of distributed computation nodes.

Keywords

Grid computing distributed computing computational biology biological sequence alignment 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Nova Ahmed
    • 1
  • Yi Pan
    • 1
  • Art Vandenberg
    • 1
  1. 1.Georgia State UniversityAtlantaUSA

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