Modeling Now Stochastically the free Energy of RNA

This webservice allows the user to

  • upload a textfile that contains RNA sequences together with the corresponding secondary structures (encoded in bar bracket notation, an example can be found here);
  • this data is used to train a stochastic context-free grammar according to the Maximum Likelihood principle and
  • to determine averages of length dependent contributions to the free energy (e.g. contributions of hairpin loops) according to Turner's model.
Those averages together with the trained grammar are used afterwards to compute precise asymptotics for the expected free energy as a function of the sequence length and the corresponding variances. A PDF file is generated which comprises all the results computed (here is the output that would be generated using above example input).

Since the computations to be performed are rather time-consuming they are submitted to a queue; the output will eventually be provided for download. If you make use of this service for your own research, please cite the following paper.