Pseudoknot-generating operation

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationSOFSEM 2016
Subtitle of host publicationTheory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings
EditorsRūsiņš Mārtiņš Freivalds, Gregor Engels, Barbara Catania
PublisherSpringer Verlag
Pages241-252
Number of pages12
ISBN (Print)9783662491911
DOIs
Publication statusPublished - 2016
Event42nd International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2016 - Harrachov, Czech Republic
Duration: 2016 Jan 232016 Jan 28

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9587
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other42nd International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2016
CountryCzech Republic
CityHarrachov
Period16/1/2316/1/28

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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  • Cite this

    Cho, D. J., Han, Y. S., Ng, T., & Salomaa, K. (2016). Pseudoknot-generating operation. In R. M. Freivalds, G. Engels, & B. Catania (Eds.), SOFSEM 2016: Theory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings (pp. 241-252). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9587). Springer Verlag. https://doi.org/10.1007/978-3-662-49192-8_20