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Nucleic Acids Research 2005 33(2):519-524; doi:10.1093/nar/gkh983
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Published online 26 January 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation

D. M. Layton and R. Bundschuh*

Department of Physics, The Ohio State University 174 W 18th Avenue, Columbus, OH 43210-1106, USA

*To whom correspondence should be addressed. Tel: +1 614 688 3978; Fax: +1 614 292 7557; Email: dlayton2{at}uiuc.edu

Received August 21, 2004. Revised November 16, 2004. Accepted November 16, 2004.

Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction algorithms are to changes in these parameters. We found already that for changes corresponding to the actual experimental error to which these parameters have been determined, 30% of the structure are falsely predicted whereas the ground state structure is preserved under parameter perturbation in only 5% of all the cases. We establish that base-pairing probabilities calculated in a thermal ensemble are viable although not a perfect measure for the reliability of the prediction of individual structure elements. Here, a new measure of stability using parameter perturbation is proposed, and its limitations are discussed.

Present address: D. M. Layton, University of Illinois at Urbana-Champaign, 1110 W Green Street, Urbana, IL 68101, USA

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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