How to predict the various helix and loops in the secondary structure
Can anyone tell me how to actually predict the secondary structure and its various features (D1-D', BoxB, V3 etc.). Mfold is used so rapidly for interpretation of new species of microbes.
The typical thing that many labs are doing is to fold the RNA and then predict that which portions are different and which are similar. But my problem is to actually know what are the various regions first in the structure that comes out as an output.
Please do contact me if my question is still not clear to you.