### 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 language | English |
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Title of host publication | SOFSEM 2016 |

Subtitle of host publication | Theory and Practice of Computer Science - 42nd International Conference on Current Trends in Theory and Practice of Computer Science, Proceedings |

Editors | Rūsiņš Mārtiņš Freivalds, Gregor Engels, Barbara Catania |

Publisher | Springer Verlag |

Pages | 241-252 |

Number of pages | 12 |

ISBN (Print) | 9783662491911 |

DOIs | |

Publication status | Published - 2016 Jan 1 |

Event | 42nd International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2016 - Harrachov, Czech Republic Duration: 2016 Jan 23 → 2016 Jan 28 |

### Publication series

Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
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Volume | 9587 |

ISSN (Print) | 0302-9743 |

ISSN (Electronic) | 1611-3349 |

### Other

Other | 42nd International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2016 |
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Country | Czech Republic |

City | Harrachov |

Period | 16/1/23 → 16/1/28 |

### Fingerprint

### All Science Journal Classification (ASJC) codes

- Theoretical Computer Science
- Computer Science(all)

### Cite this

*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

}

*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.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - Pseudoknot-generating operation

AU - Cho, Da Jung

AU - Han, Yo-Sub

AU - Ng, Timothy

AU - Salomaa, Kai

PY - 2016/1/1

Y1 - 2016/1/1

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.

UR - http://www.scopus.com/inward/record.url?scp=84956627442&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84956627442&partnerID=8YFLogxK

U2 - 10.1007/978-3-662-49192-8_20

DO - 10.1007/978-3-662-49192-8_20

M3 - Conference contribution

SN - 9783662491911

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

SP - 241

EP - 252

BT - SOFSEM 2016

A2 - Freivalds, Rūsiņš Mārtiņš

A2 - Engels, Gregor

A2 - Catania, Barbara

PB - Springer Verlag

ER -