Shuffling biological sequences with motif constraints

Authors:
Romain Rivière;Dominique Barth;Johanne Cohen;Alain Denise
Affiliations:
LRI, Univ Paris-Sud and CNRS, Orsay, F-91405, France;PRISM, Univ Versailles-St-Quentin and CNRS, Versailles, France;LORIA, Univ Nancy, CNRS and INRIA, Nancy, France;LRI, Univ Paris-Sud and CNRS, Orsay, F-91405, France
Venue:
Journal of Discrete Algorithms
Year:
2008

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Abstract

We study the following problem: given a biological sequence S, a multiset M of motifs and an integer k, generate uniformly random sequences which contain the given motifs and have exactly the same frequencies of occurrence of k-lets (i.e. factors of length k) of S. We notably prove that the problem of deciding whether a sequence respects the given motif constraints is NP-complete. Nevertheless, we give a random generation algorithm which turns out to be experimentally efficient.