Question

Three scores, Pnum (i), Hnum (i,j), and Ssum, have been derived to assist with a determination of the reliability of a secondary structure prediction for a particular base i or a base pair i,j. Which of the following is not a correct regarding Pnum?

(a) is the total number of energy dots regardless of color in the i th row and i th column of the energy dot plot

(b) is the total number of energy dots considering the color in the ith row and ith column of the energy dot plot

(c) represents in an unfiltered dot plot

(d) represents the number of base pairs

I had been asked this question during an internship interview.

Enquiry is from MFOLD and the Use of Energy Plots in division RNA Structure Prediction of Bioinformatics

Answer 1

The correct choice is (b) is the total number of energy dots considering the color in the ith row and ith column of the energy dot plot

The best explanation: It represents the number of base pairs that the ith base can form with all other base pairs in structures within the defined energy range. The lower this value, the better defined or “well determined” the local structure because there are few competitive foldings.