The PTAS of Prediction for RNA Pseudoknotted Structure

The prediction of RNA structure with pseudoknots is a nondeterministic polynomial-time hard (NP-hard) problem; according to minimum free energy models and computational methods, we investigate the RNA-pseudoknotted structure. Our paper presents an efficient algorithm for predicting RNA structure with pseudoknots, and the algorithm takes O([Formula: see text]) time and O([Formula: see text]) space, the experimental tests in Rfam10.1 and PseudoBase indicate that the algorithm is more effective and precise. The predicting accuracy, the time complexity and space complexity outperform existing algorithms, such as Maximum Weight Matching (MWM) algorithm, PKNOTS algorithm and Inner Limiting Layer (ILM) algorithm, and the algorithm can predict arbitrary pseudoknots. And there exists a [Formula: see text] ([Formula: see text]) polynomial time approximation scheme in searching maximum number of stackings, and we give the proof of the approximation scheme in RNA-pseudoknotted structure. We have improved several types of pseudoknots considered in RNA folding structure, and analyze their possible transitions between types of pseudoknots.

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A Phylogenetically Conserved Hairpin-Type 3′ Untranslated Region Pseudoknot Functions in Coronavirus RNA Replication

Journal of Virology ◽

10.1128/jvi.73.10.8349-8355.1999 ◽

1999 ◽

Vol 73 (10) ◽

pp. 8349-8355 ◽

Cited By ~ 99

Author(s):

Gwyn D. Williams ◽

Ruey-Yi Chang ◽

David A. Brian

Keyword(s):

Untranslated Region ◽

Tertiary Structure ◽

Mutational Analysis ◽

Rna Replication ◽

Regulatory Control ◽

Control Element ◽

Tertiary Structures ◽

Pseudoknotted Structure ◽

Type 3 ◽

Interfering Rna

ABSTRACT Secondary and tertiary structures in the 3′ untranslated region (UTR) of plus-strand RNA viruses have been postulated to function as control elements in RNA replication, transcription, and translation. Here we describe a 54-nucleotide (nt) hairpin-type pseudoknot within the 288-nt 3′ UTR of the bovine coronavirus genome and show by mutational analysis of both stems that the pseudoknotted structure is required for the replication of a defective interfering RNA genome. The pseudoknot is phylogenetically conserved among coronaviruses both in location and in shape but only partially in nucleotide sequence, and evolutionary covariation of bases to maintain G · U pairings indicates that it functions in the plus strand. RNase probing of synthetic transcripts provided additional evidence of its tertiary structure and also identified the possible existence of two conformational states. These results indicate that the 3′ UTR pseudoknot is involved in coronavirus RNA replication and lead us to postulate that it functions as a regulatory control element.

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