International Conference on Current Trends in Theory and Practice of Informatics

SOFSEM 2016: Theory and Practice of Computer Science pp 241-252 | Cite as

Pseudoknot-Generating Operation

Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9587)


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.


Pseudoknots Pseudoknot-generating operation Closure and decision properties Formal languages 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Da-Jung Cho
    • 1
  • Yo-Sub Han
    • 1
  • Timothy Ng
    • 2
  • Kai Salomaa
    • 2
  1. 1.Department of Computer ScienceYonsei UniversitySeoulRepublic of Korea
  2. 2.School of ComputingQueen’s UniversityKingstonCanada

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