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OJB©
Online
Journal of Bioinformatics©
Volume 5 : 49-58, 2004
1 School of Agriculture and Food
Systems,
Zou Y, Reliability of RNA secondary Structure
prediction with XNAfold, Online J Bioinformatics 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 (http://xnafold.tripod.com). 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