The cpPredictor server generates secondary structure of query sequence(s) using structural template(s). Templates are RNA secondary structures, either experimentally identified or predicted. FASTA format for sequences and dot-bracket format for the template structures are accepted on input. Biological reliability of the generated structures is evaluated in form of z-scores.
Information on how the prediction algorithm works can be found here. You can also try our example.
Citation: Panek, J., Modrak, M. and Schwarz, M. (2017) An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences, Front Genet, 8, 147.