MProfiler: A Profile-Based Method for DNA Motif Discovery

  • Doaa Altarawy
  • Mohamed A. Ismail
  • Sahar M. Ghanem
Conference paper

DOI: 10.1007/978-3-642-04031-3_2

Volume 5780 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Altarawy D., Ismail M.A., Ghanem S.M. (2009) MProfiler: A Profile-Based Method for DNA Motif Discovery. In: Kadirkamanathan V., Sanguinetti G., Girolami M., Niranjan M., Noirel J. (eds) Pattern Recognition in Bioinformatics. PRIB 2009. Lecture Notes in Computer Science, vol 5780. Springer, Berlin, Heidelberg

Abstract

Motif Finding is one of the most important tasks in gene regulation which is essential in understanding biological cell functions. Based on recent studies, the performance of current motif finders is not satisfactory. A number of ensemble methods have been proposed to enhance the accuracy of the results. Existing ensemble methods overall performance is better than stand-alone motif finders. A recent ensemble method, MotifVoter, significantly outperforms all existing stand-alone and ensemble methods. In this paper, we propose a method, MProfiler, to increase the accuracy of MotifVoter without increasing the run time by introducing an idea called center profiling. Our experiments show improvement in the quality of generated clusters over MotifVoter in both accuracy and cluster compactness. Using 56 datasets, the accuracy of the final results using our method achieves 80% improvement in correlation coefficient nCC, and 93% improvement in performance coefficient nPC over MotifVoter.

Keywords

Bioinformatics DNA Motif Finding Clustering 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Doaa Altarawy
    • 1
  • Mohamed A. Ismail
    • 1
  • Sahar M. Ghanem
    • 1
  1. 1.Computer and Systems Engineering Dept. Faculty of EngineeringAlexandria UniversityAlexandriaEgypt