PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences.
18.11.2010
Seemann SE, Richter AS, Gesell T, Backofen R, Gorodkin J.
Bioinformatics. 2011;27(2):211-9
Predicting RNA-RNA interactions is essential for determining the function of non-coding RNAs. Our method PETcofold predicts conserved intereactions and secondary structures of two multiple alignments of RNA sequences taking covariance information into account.
We show for several eukaryotic and bacterial RNAs and their targets that the prediction can be improved by our comparative approach. PETcofold was also evaluated on data with phylogenetically simulated sequences, where we observed increased performance with increased covariance.
