Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
4951944 | Theoretical Computer Science | 2017 | 27 Pages |
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.
Keywords
Related Topics
Physical Sciences and Engineering
Computer Science
Computational Theory and Mathematics
Authors
Da-Jung Cho, Yo-Sub Han, Timothy Ng, Kai Salomaa,