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Prediction of Binding Sites in the Mouse Genome Using Support Vector Machines

  • Yi Sun
  • Mark Robinson
  • Rod Adams
  • Alistair Rust
  • Neil Davey
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5164)

Abstract

Computational prediction of cis-regulatory binding sites is widely acknowledged as a difficult task. There are many different algorithms for searching for binding sites in current use. However, most of them produce a high rate of false positive predictions. Moreover, many algorithmic approaches are inherently constrained with respect to the range of binding sites that they can be expected to reliably predict. We propose to use SVMs to predict binding sites from multiple sources of evidence. We combine random selection under-sampling and the synthetic minority over-sampling technique to deal with the imbalanced nature of the data. In addition, we remove some of the final predicted binding sites on the basis of their biological plausibility. The results show that we can generate a new prediction that significantly improves on the performance of any one of the individual prediction algorithms.

Keywords

Support Vector Machine Mouse Genome Post Processing Minority Class False Positive Prediction 
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 Berlin Heidelberg 2008

Authors and Affiliations

  • Yi Sun
    • 1
  • Mark Robinson
    • 2
  • Rod Adams
    • 1
  • Alistair Rust
    • 3
  • Neil Davey
    • 1
  1. 1.Science and technology research schoolUniversity of HertfordshireUnited Kingdom
  2. 2.Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUSA
  3. 3.Institute for Systems BiologySeattleUSA

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