This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Ab Initio Approach”.

1. In dot matrix in ab initio methods, the diagonals _____ to the main diagonal represent regions that can self hybridize.

a) parallel

b) cutting in random fashion

c) perpendicular

d) adjacent parallel

View Answer

Explanation: The diagonals perpendicular to the main diagonal represent regions that can self hybridize to form double-stranded structure with traditional A–U and G–C base pairs. In reality, the pattern detection in a dot matrix is often obscured by high noise levels.

2. In dot matrix in ab initio methods, one way to reduce the noise in the matrix is to select an appropriate window size of a maximum number of contiguous base matches.

a) True

b) False

View Answer

Explanation: to reduce the noise in the matrix is to select an appropriate window size of a minimum number of contiguous base matches. Normally, only a window size of four consecutive base matches is used. If the dot plot reveals more than one feasible structure, the lowest energy one is chosen.

3. 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

View Answer

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.

4. In ab initio methods, a quantitative approach such as dynamic programming can be used to assemble a final structure with optimal base-paired regions.

a) True

b) False

View Answer

Explanation: In this approach, an RNA sequence is compared with itself. A scoring scheme is applied to fill the matrix with match scores based on Watson–Crick base complementarity.

5. In dynamic programming, in ab initio methods, Often, ____ base pairing and energy terms of the base pairing _____ incorporated into the scoring process.

a) G-C, are

b) G–U, are not

c) G–U, are also

d) G-C, are not

View Answer

Explanation: Although the traditional structure comprises of A–U and G–C base pairs, G-U base pairing is incorporated into the scoring process. A path with the maximal score within a scoring matrix after taking into account the entire sequence information represents the most probable secondary structure form.

6. The dynamic programming method produces ____ structure with _____ score.

a) one, single best

b) multiple, single best

c) multiple, multiple

d) single, multiple

View Answer

Explanation: However, this is potentially a drawback of this approach. In reality an RNA may exist in multiple alternative forms with near minimum energy but not necessarily the one with maximum base pairs.

7. The problem of dynamic programming to select one single structure can be complemented by adding a probability distribution function, known as the _________ which calculates a mathematical distribution of probable base pairs in a thermodynamic equilibrium.

a) partition function

b) division function

c) increment function

d) fold function

View Answer

Explanation: This function helps to select a number of suboptimal structures within a certain energy range. The MFOLD and RNAFold are two well-known programs using the ab initio prediction method.

8. Which of following is correct about MFOLD?

a) It uses the dynamic programming only

b) It uses the thermodynamic calculations only

c) It uses the both dynamic programming and thermodynamic calculations as well

d) It doesn’t take into account the themoststablility of the secondary structures

View Answer

Explanation: It is a web-based program for RNA secondary structure prediction. It combines dynamic programming and thermodynamic calculations for identifying themostable secondary structures with the lowest energy. It also produces dot plots coupled with energy terms. This method is reliable for short sequences, but becomes less accurate as the sequence length increases.

9. Like Mfold, RNAfold only examines the energy terms of the optimal alignment in a dot plot.

a) True

b) False

View Answer

Explanation: is one of the web programs in the Vienna package. Unlike Mfold, which only examines the energy terms of the optimal alignment in a dot plot, RNAfold extends the sequence alignment to the vicinity of the optimal diagonals to calculate thermodynamic stability of alternative structures.

10. Which of the following about the RNAFold is incorrect?

a) It extends the sequence alignment to the vicinity of the optimal diagonals to calculate thermodynamic stability of alternative structures

b) It incorporates a partition function

c) It doesn’t necessarily use a partition function

d) It aims to select a number of statistically most probable structures in one of its steps

View Answer

Explanation: Based on both thermodynamic calculations and the partition function, a number of alternative structures that may be suboptimal are provided. The collection of the predicted structures may provide a better estimate of plausible foldings of an RNA molecule than the predictions by Mfold.

**Sanfoundry Global Education & Learning Series – Bioinformatics.**

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