Bioinformatics Questions and Answers – Limitations of Prediction

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This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Limitations of Prediction”.

1. Which of the following is incorrect about the RNA structure prediction?
a) Given the sequence, it provides an ab initio prediction of secondary structure
b) From the many possible choices of complementary sequences that can potentially base-pair, the compatible sets that provide the highest energy molecules are chosen
c) Structures with energies almost as stable as the most stable one may also be produced
d) Regions whose predictions are the most reliable can be identified from such an analysis
View Answer

Answer: b
Explanation: Stable structures are the ones with least or relatively quite low energy. Sequence variations found in related sequences may also be used to predict which base pairs are likely to be found in each of the molecules. One variation of RNA structure prediction methods will predict a set of sequences that are able to form a particular structure.
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2. A type of RNA secondary structure prediction method takes into account conserved patterns of base-pairing that are conserved during evolution of a given class of RNA molecules.
a) True
b) False
View Answer

Answer: a
Explanation: Sequence positions that base-pair are found to vary at the same time during evolution of RNA molecules so that structural integrity is maintained. For example, if two positions G and C form a base pair in a given type of molecule, then sequences that have C and G reversed, or A and U or U and A at the corresponding positions, would be considered reasonable matches.

3. RNA secondary structure is composed primarily of triple-stranded RNA regions formed by folding the single-stranded molecule back twice on itself.
a) True
b) False
View Answer

Answer: b
Explanation: RNA secondary structure is composed primarily of double-stranded RNA regions formed by folding the single-stranded molecule back on itself. To produce such double-stranded regions, a run of bases downstream in the RNA sequence must be complementary to another upstream run so that Watson–Crick base-pairing between the complementary nucleotides G/C and A/U (analogous to the G/C and A/T base pairs in DNA) can occur.

4. ____ wobble pairs may be produced in these double-stranded regions.
a) A/A
b) A/U
c) G/C
d) G/U
View Answer

Answer: d
Explanation: As in DNA, the G/C base pairs contribute the greatest energetic stability to the molecule, with A/U base pairs contributing less stability than G/C, and G/U wobble base pairs contributing the least. From the RNA structures that have been solved, these base pairs and a number of additional ones have been identified.

5. In predicting RNA secondary structure, some simplifying assumptions are usually made, like the _____ structure is similar to the _____
a) most likely, energetically most unstable structure
b) most unlikely, energetically most stable structure
c) most likely, energetically most stable structure
d) least likely, energetically most stable structure
View Answer

Answer: c
Explanation: The assumption here is that the most predicted or likely structure has to be similar to the energetically most stable structure. The abundance is not taken into consideration in this.
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6. The Second assumption in predicting RNA secondary structure is that the energy associated with any position in the structure is _____ influenced by local sequence and structure.
a) only
b) not at all
c) partially
d) never
View Answer

Answer: a
Explanation: The energy associated with a particular base pair in a double-stranded region is assumed to be influenced only by the previous base pair and not by the base pairs farther down the double-stranded region or anywhere else in the structure. These energies can be reliably estimated by experimentation with small, synthetic RNA oligonucleotides recently improved to include sequence dependence.

7. The third assumption in predicting RNA secondary structure is that the structure is assumed to be formed by _____ of the chain back on itself in a manner that ________
a) crossing, produces knots
b) crossing, does not produce any knots
c) folding, produces knots
d) folding, does not produce any knots
View Answer

Answer: d
Explanation: The best way of representing this requirement is to draw the sequence in a circular form. The paired bases are then joined by arcs. If the total structure with all predicted base pairs is to be free of knots, none of the arcs must cross.

8. Martinez (1984) made a list of possible double-stranded regions, and these regions were then given weights in proportion to their equilibrium constants, calculated by ______
a) the Boltzmann function [exp (-∆G/RT2)]
b) the Boltzmann function [exp (-∆G/RT)]
c) the Boltzmann function [exp (-∆G/RT -T)]
d) the Boltzmann function [exp (∆G/RT)]
View Answer

Answer: b
Explanation: Here, the (-∆G) is the free energy of the regions, R is the gas constant, and T is the temperature. The RNA molecule is folded by a Monte Carlo method in which one initial region is chosen at random from a weighted pool, similar to the method used in Gibbs sampling.

9. In 1971, first estimation of the energy associated with regions of secondary structure by extrapolation from studies with small molecules was done and then an attempt was made to predict which configurations of larger molecules were the most energetically stable.
a) True
b) False
View Answer

Answer: a
Explanation: Energy estimates included the stabilizing energy associated with stacking base pairs in a double-stranded region and the destabilizing influence of regions that were not paired. Pipas and McMahon (1975) developed computer programs that listed all possible helical regions in tRNA sequences.
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10. Nussinov and Jacobson (1980) were the first to design a precise and efficient algorithm for predicting secondary structure.
a) True
b) False
View Answer

Answer: a
Explanation: The algorithm generates two scoring matrices—one M (i,j) to keep track of the maximum number of base pairs that can be formed in any interval i to j in the sequence. The second K (i,j) is to keep track of the base position k that is paired with j.

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Manish Bhojasia, a technology veteran with 20+ years @ Cisco & Wipro, is Founder and CTO at Sanfoundry. He is Linux Kernel Developer & SAN Architect and is passionate about competency developments in these areas. He lives in Bangalore and delivers focused training sessions to IT professionals in Linux Kernel, Linux Debugging, Linux Device Drivers, Linux Networking, Linux Storage, Advanced C Programming, SAN Storage Technologies, SCSI Internals & Storage Protocols such as iSCSI & Fiber Channel. Stay connected with him @ LinkedIn