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PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

By Stefan E. Seemann, Andreas S. Richter, Tanja Gesell and Rolf Backofen


Motivation: Predicting RNA-RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods for the prediction of interactions are all based on single sequences. Since comparative methods have already been useful in RNA structure determination, we assume that conserved RNA-RNA interactions also imply conserved function. Of these we further assume that a non-negligible amount of the existing RNA-RNA interactions have also acquired compensating base changes throughout evolution. We implement a method, PETcofold, that can take covariance information in intra-molecular and inter-molecular base pairs into account to predict interactions and secondary structures of two multiple alignments of RNA sequences. Results: PETcofold’s ability to predict RNA-RNA interactions was evaluated on a carefully curated data set of 32 bacterial smal

Year: 2011
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