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.
Loading...