Question

A limitation of the Zuker method and other methods (Nakaya et al. 1995) for computing suboptimal RNA structures is that they do not compute all the structures within a given energy range of the minimum free-energy structure.

(a) True

(b) False

The question was asked during an interview for a job.

The origin of the question is MFOLD and the Use of Energy Plots topic in portion RNA Structure Prediction of Bioinformatics

Answer 1

Right option is (a) True

The explanation: For example, no alternative structures are produced that have the absence of base pairs in the best structure, and, if two substructures are joined by a stretch of unpaired bases, no structures are produced that are suboptimal for both structures. These factors limit the number of alternative structures predicted compared to known variations based on sequence variations in tRNAs.