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Finding Protein Binding Sites Using Volunteer Computing Grids

  • Travis DesellEmail author
  • Lee A. Newberg
  • Malik Magdon-Ismail
  • Boleslaw K. Szymanski
  • William Thompson
Part of the Advances in Intelligent and Soft Computing book series (AINSC, volume 144)

Abstract

This paper describes initial work in the development of the DNA@Home volunteer computing project, which aims to use Gibbs sampling for the identification and location of DNA control signals on full genome scale data sets. Most current research involving sequence analysis for these control signals involve significantly smaller data sets, however volunteer computing can provide the necessary computational power to make full genome analysis feasible. A fault tolerant and asynchronous implementation of Gibbs sampling using the Berkeley Open Infrastructure for Network Computing (BOINC) is presented, which is currently being used to analyze the intergenic regions of the Mycobacterium tuberculosis genome. In only three months of limited operation, the project has had over 1,800 volunteered computing hosts participate and obtains a number of samples required for analysis over 400 times faster than an average computing host for the Mycobacterium tuberculosis dataset. We feel that the preliminary results for this project provide a strong argument for the feasibility and public interest of a volunteer computing project for this type of bioinformatics.

Keywords

Intergenic Region Full Genome Motif Model Yersinia Pestis Gibbs Sampling Algorithm 
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 GmbH Berlin Heidelberg 2012

Authors and Affiliations

  • Travis Desell
    • 1
    Email author
  • Lee A. Newberg
    • 2
  • Malik Magdon-Ismail
    • 2
  • Boleslaw K. Szymanski
    • 2
  • William Thompson
    • 3
  1. 1.University of North DakotaGrand ForksUSA
  2. 2.RPITroyUSA
  3. 3.Center for Computational Molecular Biology, Department of Applied MathematicsBrown UniversityProvidenceUSA

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