The Program RNAfold

Our first task will be to do a structure prediction using RNAfold. This should get you familiar with the input and output format as well as the graphical output produced.

RNAfold reads RNA sequences from stdin, calculates their minimum free energy (MFE) structure, prints the MFE structure in dot-bracket notation and its free energy to stdout. If the -p option is set it also computes the partition function, the base pairing probability matrix and additionally prints the free energy of the thermodynamic ensemble, the frequency of the MFE structure in the ensemble and the ensemble diversity to stdout. Another useful option is the -MEA option, which also shows the maximum expected accuracy, but remember that this also needs more CPU time then without -MEA.