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 Jan 1
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

Fingerprint

Formal languages
RNA
Regular Languages
Context free languages
Finite automata
Strings
Molecular structure
Deterministic Finite Automata
Context-free Languages
DNA
Polynomials
Polynomial-time Algorithm
Closure
Encoding
Efficient Algorithms
Predict

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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
Cho, Da Jung ; Han, Yo-Sub ; Ng, Timothy ; Salomaa, Kai. / Pseudoknot-generating operation. SOFSEM 2016: Theory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings. editor / Rūsiņš Mārtiņš Freivalds ; Gregor Engels ; Barbara Catania. Springer Verlag, 2016. pp. 241-252 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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Cho, DJ, Han, Y-S, Ng, T & Salomaa, K 2016, Pseudoknot-generating operation. in RM 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. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 9587, Springer Verlag, pp. 241-252, 42nd International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2016, Harrachov, Czech Republic, 16/1/23. https://doi.org/10.1007/978-3-662-49192-8_20

Pseudoknot-generating operation. / Cho, Da Jung; Han, Yo-Sub; Ng, Timothy; Salomaa, Kai.

SOFSEM 2016: Theory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings. ed. / Rūsiņš Mārtiņš Freivalds; Gregor Engels; Barbara Catania. Springer Verlag, 2016. p. 241-252 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9587).

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

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AU - Salomaa, Kai

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N2 - 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.

AB - 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.

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T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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