Scaling up Genome Similarity Search Services through Content Distribution

  • Authors:

  • Chen Wang;Bing Bing Zhou;Albert Y. Zomaya

  • Affiliations:

  • University of Sydney, Australia;University of Sydney, Australia;University of Sydney, Australia

  • Venue:
  • ICPP '07 Proceedings of the 2007 International Conference on Parallel Processing
  • Year:
  • 2007

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Abstract

As the increase of genome database size, there are increasing number of methods for detecting sequence similarity and increasing demands for genome sequence search and alignment services. It is a challenge to scale up the computer systems for serving these demands in a timely manner. This paper tackles this problem from a novel perspective, which treats the sequence search requests as content requests to both genome databases and similarity detection methods; therefore, scaling up the computer systems that serve these contents is a process of constructing content distribution network. The paper gives a decentralized method to construct content distribution network for a variety of genome sequence similarity detection services. It also gives a scheduling algorithm for efficiently using content nodes. Our simulation results show that scalability and high content node utilization can be achieved in such a system while the costs of achieving these are controllable.