Bioinformatics Multiple Choice Questions on “Ab Initio Approach”.
1. In dot matrix in ab initio methods, the diagonals _____________ to the main diagonal represent regions that can self hybridize. Answer: c 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. Answer: B 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. Answer: c 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. Answer: A 5. In dynamic programming, in ab initio methods, Often ________ base pairing and energy terms of the base pairing _____ incorporated into the scoring process. Answer: c 6. The dynamic programming method produces ____ structure with _____ score. Answer: A 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 thermodynamic equilibrium. Answer: A 8. Which of the following is correct about MFOLD? Answer: B 9. Like Mfold, RNAfold only examines the energy terms of the optimal alignment in a dot plot. Answer: B 10. Which of the following about the RNAFold is incorrect? Answer: c
A. parallel
B. cutting in random fashion
C. perpendicular
D. adjacent parallel
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.
A. True
B. False
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.
A. multiple, large
B. single, large
C. single, small
D. multiple, small
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.
A. True
B. False
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.
A. G-C, are
B. G–U, are not
C. G–U, are also
D. G-C, are not
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.
A. one, single best
B. multiple, single best
C. multiple, multiple
D. single, multiple
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.
A. partition function
B. division function
C. increment function
D. fold function
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.
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
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.
A. True
B. False
Explanation: It 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.
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
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.