Shuffling biological sequencess with motifs constraints

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 occurrences of k-lets (i.e. factors of length k) of S. This question involves difficult problems: We notably state that the problem of deciding whether a sequence respects given motifs constraints is NP-complete. Meanwhile, we give a random generation algorithm which turns out to be experimentally efficient.
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Dominique Barth, Johanne Cohen, Alain Denise, Romain Rivière. Shuffling biological sequencess with motifs constraints. Algorithms and Computational Methods for Biochemical and Evolutionary Networks - CompBioNets'2004, Dec 2004, Recife, Brazil. 18 p. ⟨inria-00099891⟩

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