Combinatorial RNA Design: Designability and Structure-Approximating Algorithm

Jozef Haleš 1 Ján Maňuch 2, 1 Yann Ponty 3, 4, 1 Ladislav Stacho 1
4 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete characterizations for the structures that can be designed using restricted alphabets. Under a classic four-letter alphabet, we provide a complete characterization of designable structures without unpaired bases. When unpaired bases are allowed, we provide partial characterizations for classes of designable/undesignable structures, and show that the class of designable structures is closed under the stutter operation. Membership of a given structure to any of the classes can be tested in linear time and, for positive instances, a solution can be found in linear time. Finally, we consider a structure-approximating version of the problem that allows to extend bands (helices) and, assuming that the input structure avoids two motifs, we provide a linear-time algorithm that produces a designable structure with at most twice more base pairs than the input structure.
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Conference papers
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https://hal.inria.fr/hal-01115349
Contributor : Yann Ponty <>
Submitted on : Tuesday, February 10, 2015 - 8:42:25 PM
Last modification on : Wednesday, March 27, 2019 - 4:41:29 PM
Long-term archiving on : Thursday, May 28, 2015 - 9:40:59 AM

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  • HAL Id : hal-01115349, version 1
  • ARXIV : 1502.03201

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Jozef Haleš, Ján Maňuch, Yann Ponty, Ladislav Stacho. Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun 2015, Ischia Island, Italy. ⟨hal-01115349v1⟩

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