Abstract
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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Haleš, J., Maňuch, J., Ponty, Y., Stacho, L. (2015). Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. In: Cicalese, F., Porat, E., Vaccaro, U. (eds) Combinatorial Pattern Matching. CPM 2015. Lecture Notes in Computer Science(), vol 9133. Springer, Cham. https://doi.org/10.1007/978-3-319-19929-0_20
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DOI: https://doi.org/10.1007/978-3-319-19929-0_20
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