Bioinformatics Advance Access originally published online on February 12, 2004
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Bioinformatics 20(10) © Oxford University Press 2004; all rights reserved.
Evaluating the predictability of conformational switching in RNA
1 International NRW Graduate School in Bioinformatics and Genome Research and 2 Institute for Bioinformatics, Bielefeld University, P.O. Box 100 131, 33501 Bielefeld, Germany
Received on September 25, 2003; accepted on December 15, 2003
Advance Access Publication February 12, 2004
Motivation: There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural switching in RNA. It is based on three hypotheses about the secondary structure space of a switching RNA molecule that can be evaluated by RNA folding and structure comparison. In the positive case, the predicted structural switching must be verified experimentally.
Results: After reviewing the strategy used in paRNAss, we present recent improvements on the algorithmic level of the approach, and the results of an evaluation procedure, comprising 1500 RNA sequences. It could be shown that the paRNAss approach performs well on known examples for conformational switching in RNA. The overall number of positive predictions was small, whereas for human 3' UTRs, representing regulatory important regions, it was substantially higher than for arbitrary natural and random sequences.
Availability: paRNAss is available as a Web service at http://bibiserv.techfak.uni-bielefeld.de/parnass
Supplementary information: Detailed information on the analyses summarized in Table 1 can be found at http://bibiserv.techfak.uni-bielefeld.de/parnass/examples.html
Contact: bvoss{at}techfak.uni-bielefeld.de
* To whom correspondence should be addressed.
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