Question

In the programs related to FOLD, the second region, the ________ region, is used to calculate the energy of the ________ structure.

(a) included, most likely

(b) included, best

(c) excluded, least likely

(d) excluded, best

This question was addressed to me during an online interview.

Asked question is from MFOLD and the Use of Energy Plots in section RNA Structure Prediction of Bioinformatics

Answer 1

Right option is (d) excluded, best

Explanation: A second region, the excluded region, is used to calculate the energy of the best structure that includes i, j but is not derived from the structure at i+1, j-1 After certain corrections are made, the difference between the included and excluded values is the most energetic structure that includes the base pair i, j.