RNA Secondary Structure Prediction Algorithms Including Pseudoknots

ISSN: 2212-392X (Online)
ISSN: 1574-8936 (Print)

Volume 11, 5 Issues, 2016

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Current Bioinformatics

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Yi-Ping Phoebe Chen
Department of Computer Science and Information Technology
La Trobe University

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RNA Secondary Structure Prediction Algorithms Including Pseudoknots

Current Bioinformatics, 9(3): 268-283.

Author(s): Dolly Sharma, Shailendra Singh and Trilok Chand.

Affiliation: Department of Computer Science and Engineering, PEC University of Technology, Chandigarh, India.


Pseudoknot is an important motif in RNA secondary structure. Early researchers of RNA secondary structure prediction ignored pseudoknots, but now pseudoknot is in focus in RNA secondary structure prediction. Several algorithms like dynamic programming, comparative algorithms, heuristic algorithms, formal grammar algorithms etc have so far been used for pseudoknot prediction, but the prediction of arbitrary pseudoknots is still an open problem. Also, there does not exist standard categorization of pseudoknot types. This article provides a brief description and comparison of various algorithms being used in pseudoknot prediction along with an overview of various forms of pseudoknots and their representations.


Comparative algorithm, dynamic programming, formal grammar, heuristics, pseudoknot, RNA secondary structure.

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Article Details

Volume: 9
Issue Number: 3
First Page: 268
Last Page: 283
Page Count: 16
DOI: 10.2174/15748936113086660010

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