Question

Which of the following is incorrect about the prediction of RNA secondary structure?

(a) Every base is first compared to every other base by a type of analysis very similar to the dot matrix analysis

(b) A row of matches in the RNA matrix indicates a succession of complementary nucleotides that can potentially form a double-stranded region

(c) A row of matches in the RNA matrix indicates a failure of complementary nucleotides that can potentially form a double-stranded region

(d) The sequence is listed across the top and down the side of the page, and G/C, A/U, and G/U base pairs are scored

This question was posed to me in homework.

My question is taken from Minimum Free in division RNA Structure Prediction of Bioinformatics

Answer 1

Correct option is (c) A row of matches in the RNA matrix indicates a failure of complementary nucleotides that can potentially form a double-stranded region

Explanation: The energy of each predicted structure is estimated by the nearest- neighbor rule by summing the negative base-stacking energies for each pair of bases in double-stranded regions. By adding the estimated positive energies of destabilizing regions such as loops at the end of hairpins, bulges within hairpins, internal bulges, and other unpaired regions.