Pseudoknot-generating operation

Da Jung Cho, Yo Sub Han, Timothy Ng, Kai Salomaa

Research output: Contribution to journalArticlepeer-review


A pseudoknot is a crucial intra-molecular structure formed primarily in RNA strands and closely related to important biological processes. This motivates us to define an operation that generates all pseudoknots from a given sequence and consider algorithmic and language theoretic properties of the operation. We design an efficient algorithm that decides whether or not a given string is a pseudoknot of a regular language L. Our algorithm runs in linear time if L is given by a deterministic finite automaton. We study closure and decision properties of the pseudoknot-generating operation. For DNA encoding applications, pseudoknot structures are undesirable. We give polynomial-time algorithms that check whether or not 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.

Original languageEnglish
Pages (from-to)52-64
Number of pages13
JournalTheoretical Computer Science
Publication statusPublished - 2017 Oct 5

Bibliographical note

Funding Information:
Cho and Han were supported by the Basic Science Research Program through NRF funded by MEST (2015R1D1A1A01060097), the Yonsei University Future-leading Research Initiative of 2016 and the IITP grant funded by the Korea government (MSIP) (R0124-16-0002), and Ng and Salomaa were supported by the Natural Sciences and Engineering Research Council of Canada Grant OGP0147224.

Publisher Copyright:
© 2017 Elsevier B.V.

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)


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