Pseudoknot-generating operation

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

Research output: Contribution to journalArticle

Abstract

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
Volume696
DOIs
Publication statusPublished - 2017 Oct 5

Fingerprint

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

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Cho, Da Jung ; Han, Yo Sub ; Ng, Timothy ; Salomaa, Kai. / Pseudoknot-generating operation. In: Theoretical Computer Science. 2017 ; Vol. 696. pp. 52-64.
@article{b23f49b9181940ab976d8a5a408913ff,
title = "Pseudoknot-generating operation",
abstract = "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.",
author = "Cho, {Da Jung} and Han, {Yo Sub} and Timothy Ng and Kai Salomaa",
year = "2017",
month = "10",
day = "5",
doi = "10.1016/j.tcs.2017.07.001",
language = "English",
volume = "696",
pages = "52--64",
journal = "Theoretical Computer Science",
issn = "0304-3975",
publisher = "Elsevier",

}

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

In: Theoretical Computer Science, Vol. 696, 05.10.2017, p. 52-64.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Pseudoknot-generating operation

AU - Cho, Da Jung

AU - Han, Yo Sub

AU - Ng, Timothy

AU - Salomaa, Kai

PY - 2017/10/5

Y1 - 2017/10/5

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85025470695&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85025470695&partnerID=8YFLogxK

U2 - 10.1016/j.tcs.2017.07.001

DO - 10.1016/j.tcs.2017.07.001

M3 - Article

AN - SCOPUS:85025470695

VL - 696

SP - 52

EP - 64

JO - Theoretical Computer Science

JF - Theoretical Computer Science

SN - 0304-3975

ER -