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 Hnum?

(a) is the sum of Pnum(i) and Pnum(j) -1

(b) is the sum of Pnum(i) and Pnum(j) + 1

(c) is the total number of dots in the ith row and jth column

(d) represents the total number of base pairs with the ith or jth base in the predicted structures

I had been asked this question in an interview.

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

Answer 1

The correct choice is (b) is the sum of Pnum(i) and Pnum(j) + 1

The explanation: The Hnum for a double stranded region is the average Hnum value for the base pairs in that helix. The lower this number, the more well determined the double-stranded region.