A pseudoknot is an intra-molecular structure formed primarily in RNA strands and much research has been done to predict efficiently pseudoknot structures in RNA. We define an operation that generates all pseudoknots from a given sequence and consider algorithmic and language theoretic properties of the operation.We give an efficient algorithm to decide whether a given string is a pseudoknot of a regular language L—the runtime is linear if L is given by a deterministic finite automaton. We consider closure and decision properties of the pseudoknot-generating operation. For DNA encoding applications, pseudoknot structures are undesirable. We give polynomial-time algorithms to decide whether a regular language L contains a pseudoknot or a pseudoknot generated by some string of L. Furthermore, we show that the corresponding questions for context-free languages are undecidable.
CITATION STYLE
Cho, D. J., Han, Y. S., Ng, T., & Salomaa, K. (2016). Pseudoknot-generating operation. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 9587, pp. 241–252). Springer Verlag. https://doi.org/10.1007/978-3-662-49192-8_20
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