This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “MFOLD and the Use of Energy Plots”.

1. Originally, the FOLD program of _____ predicted _____ having the minimum free energy.

a) M. Zuker, two structures

b) M. Wunsch, two structures

c) M. Zuker, only one

d) M. Wunsch, only one

View Answer

Explanation: However, changes in a single nucleotide can result in drastic changes in the predicted structure. A later version, called MFOLD, has improved prediction of non-base paired interactions and predicts several structures having energies close to the minimum free energy.

2. To find suboptimal structures, the dynamic programming method was modified.

a) True

b) False

View Answer

Explanation: It was so done to evaluate parts of a new scoring matrix in which the sequence is represented in two tandem copies on both the vertical and horizontal axes. The regions from i 1 to n and j 1 to n are used to calculate an energy V (i,j) for the best structure that includes an i, j base pair and is called the included region.

3. In the programs related to FOLD, the second region, the ________ region, is used to calculate the energy of the ________ structure.

a) included, most likely

b) included, best

c) excluded, least likely

d) excluded, best

View Answer

Explanation: A second region, the excluded region, is used to calculate the energy of the best structure that includes i, j but is not derived from the structure at i+1, j-1 After certain corrections are made, the difference between the included and excluded values is the most energetic structure that includes the base pair i, j.

4. In the programs related to FOLD, All complementary base pairs can be sampled in a fashion to determine which are present in a suboptimal structure.

a) True

b) False

View Answer

Explanation: All complementary base pairs can be sampled in a fashion to determine which are within a certain range of the optimal one. An energy dot plot is produced showing the locations of alternative base pairs that produce the most stable or suboptimally stable structures.

5. The program may be instructed to find structures within a certain percentage of the minimum free energy.

a) True

b) False

View Answer

Explanation: Parameter d provides a measure of similarity between two structures. When MFOLD is established on a suitable local host machine, the window is interactive, and clicking a part of the display will lead to program output of the corresponding structure.

6. 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 Pnum?

a) is the total number of energy dots regardless of color in the i th row and i th column of the energy dot plot

b) is the total number of energy dots considering the color in the ith row and ith column of the energy dot plot

c) represents in an unfiltered dot plot

d) represents the number of base pairs

View Answer

Explanation: It represents the number of base pairs that the ith base can form with all other base pairs in structures within the defined energy range. The lower this value, the better defined or “well determined” the local structure because there are few competitive foldings.

7. 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

View Answer

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.

8. 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 Ssum?

a) is also called as ss-count

b) is the number of foldings in which base i is single-stranded divided by m, the number of folding

c) is the number of foldings in which base i is single-stranded multiplied by m, the number of folding

d) gives the probability that base i is single-stranded

View Answer

Explanation: If Snum is approximately 1, then base i is probably in a single-stranded region, and if Snum is approximately 0, then base i is probably not in such a region. This reliability information has been used to annotate output files of MFOLD and other RNA display programs.

9. A limitation of the Zuker method and other methods (Nakaya et al. 1995) for computing suboptimal RNA structures is that they do not compute all the structures within a given energy range of the minimum free-energy structure.

a) True

b) False

View Answer

Explanation: For example, no alternative structures are produced that have the absence of base pairs in the best structure, and, if two substructures are joined by a stretch of unpaired bases, no structures are produced that are suboptimal for both structures. These factors limit the number of alternative structures predicted compared to known variations based on sequence variations in tRNAs.

10. These limitations of the Zuker method and other methods have been largely overcome by using an algorithm originally described by Waterman and Byers (1985) for finding sequence alignments within a certain range of the optimal one by modifications of the trace-back procedure used in dynamic programming.

a) True

b) False

View Answer

Explanation: This method efficiently calculates a large number of alternative structures, up to a very large number, within a given energy range of the minimum free-energy structure. The method has been used to demonstrate that natural tRNA sequences can form many alternative structures that are close to the minimum free-energy structure and that base modification plays a major role in this energetic stability.

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