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Nucleic Acids Research, 2003, Vol. 31, No. 13 3423-3428
© 2003 Oxford University Press

Pfold: RNA secondary structure prediction using stochastic context-free grammars

Bjarne Knudsen* and Jotun Hein1

BiRC (Bioinformatics Research Center), University of Aarhus, Høegh Guldbergsgade 10, Building 090, 8000 Århus C, Denmark 1 Department of Statistics, Oxford University, The Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, UK

*To whom correspondence should be addressed at Department of Zoology, Box 118525, University of Florida, Gainesville, FL 32611-8525, USA. Tel: +1 3523927552; Fax: +1 3523923704; Email: bk{at}birc.dk

RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs for RNA secondary structure prediction only use a single sequence at a time. This may be sufficient in some applications, but often it is possible to obtain related RNA sequences with conserved secondary structure. These should be included in structural analyses to give improved results. This work presents a practical way of predicting RNA secondary structure that is especially useful when related sequences can be obtained. The method improves a previous algorithm based on an explicit evolutionary model and a probabilistic model of structures. Predictions can be done on a web server at http://www.daimi.au.dk/~compbio/pfold.


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