Skip to Main content Skip to Navigation
Conference papers

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.
Document type :
Conference papers
Complete list of metadata

Cited literature [20 references]  Display  Hide  Download
Contributor : Publications Loria Connect in order to contact the contributor
Submitted on : Tuesday, September 26, 2006 - 10:03:36 AM
Last modification on : Wednesday, October 20, 2021 - 12:24:14 AM
Long-term archiving on: : Friday, November 25, 2016 - 12:00:17 PM


  • HAL Id : inria-00099891, version 1



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⟩



Record views


Files downloads