Pseudoknot-generating operation

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

Research output: Contribution to journalArticle


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

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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