Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamicsReport as inadecuate




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BMC Bioinformatics

, 5:104

First Online: 04 August 2004Received: 27 February 2004Accepted: 04 August 2004

Abstract

BackgroundThe general problem of RNA secondary structure prediction under the widely used thermodynamic model is known to be NP-complete when the structures considered include arbitrary pseudoknots. For restricted classes of pseudoknots, several polynomial time algorithms have been designed, where the Ontime and On space algorithm by Rivas and Eddy is currently the best available program.

ResultsWe introduce the class of canonical simple recursive pseudoknots and present an algorithm that requires On time and On space to predict the energetically optimal structure of an RNA sequence, possible containing such pseudoknots. Evaluation against a large collection of known pseudoknotted structures shows the adequacy of the canonization approach and our algorithm.

ConclusionsRNA pseudoknots of medium size can now be predicted reliably as well as efficiently by the new algorithm.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-5-104 contains supplementary material, which is available to authorized users.

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Author: Jens Reeder - Robert Giegerich

Source: https://link.springer.com/







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