RNAfold
The program reads RNA sequences, calculates their minimum free energy (mfe) structure and the mfe structure in dot-bracket notation.
If the -p option was given it also computes the partition function (pf) and base pairing probability matrix.
The dot plot of the base pairing probability matrix shows a matrix of squares with area proportional to the pairing probability in the upper right half, and one square for each pair in the minimum free energy structure in the lower left half. For each pair i-j with probability p>10E-6 there is a line of the form
i j sqrt(p) ubox
in the PostScript file, so that the pair probabilities can be easily extracted.
The sequences have to be provided in FASTA format. The first word (max. 42 char) of the FASTA header will be used for output file names. PostScript files "name_ss.ps" and "name_dp.ps" are produced for the structure and dot plot, respectively. The program will read the whole FASTA input file and provide output for each found sequence.
Input format
RNAfold requires one input file - FASTA file
Outputs