Combinatorial RNA Design: Designability and Structure-Approximating Algorithm

  • Jozef Haleš
  • Ján Maňuch
  • Yann Ponty
  • Ladislav Stacho
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9133)


In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem in which one must return an RNA sequence that admits a given secondary structure as its unique base pair maximizing structure.

First, we fully characterize designable structures using restricted alphabets. Then, under a classic four-letter alphabet, we provide a complete characterization for designable structures without unpaired bases. When unpaired bases are allowed, we characterize extensive classes of (non-)designable structures, and prove the closure of the set of designable structures under the stutter operation. Membership of a given structure to any of the classes can be tested in \(\varTheta (n)\) time, including the generation of a solution sequence for positive instances. Finally, we consider a structure-approximating version of the problem that allows to extend bands (stems). We provide a \(\varTheta (n)\) algorithm which, given a structure \(S\) avoiding two trivially non-designable motifs, transforms \(S\) into a designable structure by adding at most one base-pair to each of its stems, and returns a solution sequence.


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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Jozef Haleš
    • 1
  • Ján Maňuch
    • 1
    • 3
  • Yann Ponty
    • 1
    • 2
  • Ladislav Stacho
    • 1
  1. 1.Department of MathematicsSimon Fraser UniversityBurnabyCanada
  2. 2.Pacific Institute for Mathematical SciencesCNRS UMI3069VancouverCanada
  3. 3.Department of Computer ScienceUniversity of British ColumbiaVancouverCanada

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