I am new to RNAfold, and I have a question about it. Is there any parameter to filter out sequences producing non desiring 2nd structure? For example, the one sequence produces nice stem loop structure (please see attached image-‘seq1’) and the second sequence produces irregular stem loop structure (please see attached image-‘seq2’). So, my question is, is there any parameter (flags in RNAfold command) or filtration step to remove sequences like the second one which produces irregular or so many stem loop structures in a given secondary structure prediction?
What is your end goal, and what are you predicting the structure of?
RNAFold has a number of options for controlling the structure that it generates but it isn't designed for filtering sequences.
Maybe try setting constraints so that RNAfold will "force" the sequence to fold into the desired structure, then you can look at the free energy for each structure/sequence and look for ones with free energies that would suggest they might actually fold into that structure. This is a brute-force approach though, it could be very slow depending on your goals.
There are several programs that try and go in the other direction, you provide a structure and the program attempts to find a sequence that will fold into that structure.
