Question

In dynamic programming, in ab initio methods, the use of a dot plot can be effective in finding a ____ secondary structure in a ________ molecule.

(a) multiple, large

(b) single, large

(c) single, small

(d) multiple, small

I got this question in a national level competition.

My question is taken from Ab Initio Approach in chapter RNA Structure Prediction of Bioinformatics

Answer 1

The correct answer is (c) single, small

The explanation: Mostly, The use of a dot plot can be effective in finding a single secondary structure in a small Molecule. However, if a large molecule contains multiple secondary structure segments, choosing a combination that is energetically most stable among a large number of possibilities can be a daunting task.