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Online Journal of Bioinformatics

Volume 5:49-58, 2004.

Reliability of RNA Secondary Structure Prediction with XNAfold.


Zou Y1, 2


1School of Agriculture and Food Systems, University of Melbourne, Sneydes Road, Werribee, VIC 3030 Australia. 2School of Computer Science and Information Technology, RMIT University, VIC 3001, Australia.




Zou Y., Reliability of RNA secondary Structure prediction with XNAfold, Onl J Bioinform., 5: 49-58, 2004. Assessment of prediction reliability of RNA secondary structures remains challenging. In this paper, a direct comparison of RNA secondary structures predicted by free energy minimisation with those derived from experimentally determined three dimensional structures was carried out to assess the prediction accuracy of XNAfold ( Based on analysis of 133 different RNA sequences from the Protein Data Bank, the accuracy of secondary structure prediction was 84%. The minimum free energy structure predicted was identical to the experimentally determined structure in 58% of cases. Additionally, the experimentally determined structures matched one of the sub-optimal structures computed in 26% of cases.

Key words: RNA secondary structure, XNAfold, prediction reliability