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Toward Optimal Motif Enumeration

  • Patricia A. Evans
  • Andrew D. Smith
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2748)

Abstract

We present algorithms that reduce the time and space needed to solve problems of finding all motifs common to a set of sequences. In particular, we give algorithms that (1) require time and space linear in the size of the input, (2) succinctly encode the output so that the time and space requirements depend on the number of motifs, not directly on motif length, and (3) efficiently parallelize the enumeration.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Patricia A. Evans
    • 1
  • Andrew D. Smith
    • 1
    • 2
  1. 1.University of New BrunswickFredericton N.B.Canada
  2. 2.Ontario Cancer InstituteUniversity Health Network, Suite 703TorontoCanada

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