PMS6: A fast algorithm for motif discovery

  • Authors:

  • Shibdas Bandyopadhyay;Sartaj Sahni;Sanguthevar Rajasekaran

  • Affiliations:

  • Department of CISE, University of Florida, Gainesville, 32611, USA;Department of CISE, University of Florida, Gainesville, 32611, USA;Department of CSE, University of Connecticut, Storrs, 06269, USA

  • Venue:
  • ICCABS '12 Proceedings of the 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences
  • Year:
  • 2012

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Abstract

We propose a new algorithm, PMS6, for the (l; d)-motif discovery problem in which we are to find all strings of length l that appear in every string of a given set of strings with at most d mismatches. The run time ratio PMS5/PMS6, where PMS5 is the fastest previously known algorithm for motif discovery in large instances, ranges from a high of 2.20 for the (21,8) challenge instances to a low of 1.69 for the (17,6) challenge instances. Both PMS5 and PMS6 require some amount of preprocessing. The preprocessing time for PMS6 is 34 times faster than that for PMS5 for (23,9) instances. When preprocessing time is factored in, the run time ratio PMS5/PMS6 is as high as 2.75 for (13,4) instances and as low as 1.95 for (17,6) instances.