CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

Abstract

We corrected an error that affected our assessment of absolute and relative performance of the PETfold method. In the original version of the manuscript, results were reported for the use of unaligned RNA sequences as input for PETfold pre2.0. Jan Gorodkin and Stefan Seemann, the authors of this method (University of Copenhagen, Denmark), brought to our attention that this was incorrect, as the intended input for PETfold pre2.0 were aligned RNA sequences. Regrettably, PETfold pre2.0 did not validate the correct type of input data, and for unaligned data sets, it generated RNA secondary structure predictions, which scored poorly in our benchmark. We recalculated all predictions for PETfold pre2.0 with aligned RNA sequences (the same data sets as used for other methods that required aligned sequences). As a result, the performance of PETfold pre2.0 has significantly improved and according to the corrected rankings, this method has been re-evaluated as one of the best. Owing to the modification of relative scores calculated for PETfold pre2.0 with respect to other methods, other slight changes in the rankings occurred, which are now reflected in the corrected rankings presented on the CompaRNA Web site and in corrected Figure We apologize to the authors of PETfold as well as to the readership of Nucleic Acids Research for erroneously reporting the performance of PETfold in our original rankings. Importantly, the authors of PETfold have subsequently released a new version PETfold 2.0 that checks whether input sequences are aligned. Currently, both PETfold pre2.0 and PETfold 2.0 are tested in CompaRNA.