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 ________

crossing, does not produce any knots

folding, does not produce any knots

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?

gives the probability that base i is single-stranded

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

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

gives the probability that base i is single-stranded

Which of the following is correct about MFOLD?

It uses the both dynamic programming and thermodynamic calculations as well

It uses the dynamic programming only

It uses the thermodynamic calculations only

It uses the both dynamic programming and thermodynamic calculations as well

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

Which of the following about the RNAFold is incorrect?

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

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

It incorporates a partition function

It doesn’t necessarily use a partition function

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

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 ______

the Boltzmann function [exp (-∆G/RT -T)]

the Boltzmann function [exp (-∆G/RT²)]

the Boltzmann function [exp (-∆G/RT)]

the Boltzmann function [exp (-∆G/RT -T)]

the Boltzmann function [exp (∆G/RT)]

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?

is the total number of dots in the ith row and jth column

is the sum of Pnum(i) and Pnum(j) -1

is the sum of Pnum(i) and Pnum(j) + 1

is the total number of dots in the ith row and jth column

represents the total number of base pairs with the ith or jth base in the predicted structures

In predicting RNA secondary structure, some simplifying assumptions are usually made, like the _____ structure is similar to the _____

least likely, energetically most stable structure

most likely, energetically most unstable structure

most unlikely, energetically most stable structure

most likely, energetically most stable structure

least likely, energetically most stable structure

Which of the following is incorrect about the RNA structure prediction?

Structures with energies almost as stable as the most stable one may also be produced

Given the sequence, it provides an ab initio prediction of secondary structure

From the many possible choices of complementary sequences that can potentially base-pair, the compatible sets that provide the highest energy molecules are chosen

Structures with energies almost as stable as the most stable one may also be produced

Regions whose predictions are the most reliable can be identified from such an analysis

Which of the following is untrue about the Sfold algorithm?

It uses a unique algorithm to aid in the design of siRNA

The algorithm combines thermodynamic stabilities, calculations of target accessibility, and empirical rules

The website offers specialized programs for the design of siRNA, antisense RNA, trans-cleaving RNA, and mRNA-microRNA interactions

The website doesn’t offer programs for the design of a general program for statistically sampling suboptimal RNA structures

97 + Mcqs in Rna Secondary Structure Prediction Methods in Bioinformatics Page 1 McqOptions

1.	In a SCFG, each production of a non-terminal symbol has an associated probability for giving rise to the resulting product, and there are a set of productions, each giving a different result.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

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
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

3.	______ regions in sequences, such as those in RNA that will form secondary structures, are an example of such context-free sequences.
A.	non-interlocking
B.	non-Complementary
C.	complementary
D.	non-compatible
Answer» D. non-compatible

Discussion

4.	Through a single scoring matrix, evaluation of all the different possible configurations is done.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

5.	____ wobble pairs may be produced in these double-stranded regions.
A.	A/A
B.	A/U
C.	G/C
D.	G/U
Answer» E.

Discussion

6.	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
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

7.	Nussinov and Jacobson (1980) were the first to design a precise and efficient algorithm for predicting secondary structure.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

8.	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
Answer» D. M. Wunsch, only one

Discussion

9.	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
Answer» E.

Discussion

10.	One of the first methods used to find tRNA genes was to search for sequences that are complementary and can fold into a knot like the three found in tRNAs.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

11.	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
Answer» D. gives the probability that base i is single-stranded

Discussion

12.	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
Answer» D. G-C, are not

Discussion

13.	The dynamic programming method produces ____ structure with _____ score.
A.	one, single best
B.	multiple, single best
C.	multiple, multiple
D.	single, multiple
Answer» B. multiple, single best

Discussion

14.	Like Mfold, RNAfold only examines the energy terms of the optimal alignment in a dot plot.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

15.	Which of the 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
Answer» C. It uses the both dynamic programming and thermodynamic calculations as well

Discussion

16.	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
Answer» D. It aims to select a number of statistically most probable structures in one of its steps

Discussion

17.	The attractive interactions lead to _________ energy.
A.	increased
B.	higher
C.	lower
D.	no change in
Answer» D. no change in

Discussion

18.	Four main subtypes of secondary structures can be identified. They are hairpin loops, bulge loops, interior loops, and multi-branch loops.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

19.	The ______ refers to a structure with two ends of a single-stranded region (loop) connecting a base-paired region (stem).
A.	helical junctions
B.	hairpin loop
C.	bulge loop
D.	interior loop
Answer» C. bulge loop

Discussion

20.	The __________ refers to two single-stranded regions on opposite strands connecting two adjacent base-paired segments.
A.	hairpin loop
B.	interior loop
C.	pseudoknot loop
D.	helical junctions
Answer» C. pseudoknot loop

Discussion

21.	Base pairing, in RNA, is A–G and U–C.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

22.	The object is to find a diagonal row of matches that goes from upper left to lower right.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

23.	In comparative approach to RNA structure prediction, the Foldalign program doesn’t use the covariation information.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

24.	In comparative approach to RNA structure prediction, algorithms that do not use pre-alignment, align multiple input sequences and infers a consensus structure.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

25.	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
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

26.	In comparative approach to RNA structure prediction, Foldalign is a web-based only program for RNA alignment
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

27.	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
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

28.	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)]
Answer» C. the Boltzmann function [exp (-∆G/RT -T)]

Discussion

29.	Ab initio methods are energetically least favorable.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

30.	______ molecules can simply be identified based on their sequence similarity with already-known sequences.
A.	Larger, less conserved
B.	Larger, highly conserved
C.	smaller, highly conserved
D.	shorter, highly conserved
Answer» C. smaller, highly conserved

Discussion

31.	To find suboptimal structures, the dynamic programming method was modified.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

32.	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.
A.	partition function
B.	division function
C.	increment function
D.	fold function
Answer» B. division function

Discussion

33.	If the base pair is adjacent to loops or bulges, the neighboring loops and bulges tend to ___________ the base-pair formation.
A.	have no change on
B.	decrease the energy
C.	stabilize
D.	destabilize
Answer» E.

Discussion

34.	In ab initio approach, generally, when a base pairing is formed, the energy of the molecule is _________ because of attractive interactions between the two strands.
A.	lowered
B.	increased
C.	multiplied
D.	kept stable
Answer» B. increased

Discussion

35.	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
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

36.	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
Answer» D. adjacent parallel

Discussion

37.	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
Answer» C. is the total number of dots in the ith row and jth column

Discussion

38.	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
Answer» D. least likely, energetically most stable structure

Discussion

39.	A general theory for modeling strings of symbols, such as bases in DNA sequences, has been developed by linguists. There is a hierarchy of these so-called transformational grammars that deal with situations of increasing complexity.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

40.	If the centroid structure is different from the minimum free-energy structure, the centroid structure is often closer to the phylogenetic prediction and contains fewer base pairs, or fewer false-positive base pair predictions, than the minimum free-energy prediction.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

41.	The ILM program uses an iterative loop matching algorithm to maximize base pairs and allows pseudoknots to form by allowing base. pairs to be added or removed in successive rounds.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

42.	In comparative approach to RNA structure prediction, Dynalign is a ________ program.
A.	Windows based
B.	Fedora
C.	UNIX
D.	iOS based
Answer» D. iOS based

Discussion

43.	In addition to the canonical base pairing, there often exists non-canonical base pairing such as _________ and ________ base paring.
A.	G, U
B.	G, C
C.	U, C
D.	A, C
Answer» B. G, C

Discussion

44.	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
Answer» C. Structures with energies almost as stable as the most stable one may also be produced

Discussion

45.	The probabilistic model was used to identify small nucleolar (sno) RNAs in the yeast genome that methylate ribosomal RNA.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

46.	Which of the following is untrue about the Sfold algorithm?
A.	It uses a unique algorithm to aid in the design of siRNA
B.	The algorithm combines thermodynamic stabilities, calculations of target accessibility, and empirical rules
C.	The website offers specialized programs for the design of siRNA, antisense RNA, trans-cleaving RNA, and mRNA-microRNA interactions
D.	The website doesn’t offer programs for the design of a general program for statistically sampling suboptimal RNA structures
Answer» E.

Discussion

47.	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
Answer» B. not at all

Discussion

48.	The use of SCFGs in RNA secondary structure production analysis is in fact very similar to that of the covariance model, with the grammatical productions resembling the nodes in the ordered binary tree.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

49.	The probability model mentioned above was a hybrid combination of HMMs and SCFGs trained on sno RNAs.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

50.	The dot matrix method and the dynamic programming method can be used in detecting self-complementary regions of a sequence.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

Explore topic-wise MCQs in Bioinformatics.

In a SCFG, each production of a non-terminal symbol has an associated probability for giving rise to the resulting product, and there are a set of productions, each giving a different result.

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.

______ regions in sequences, such as those in RNA that will form secondary structures, are an example of such context-free sequences.

Through a single scoring matrix, evaluation of all the different possible configurations is done.

____ wobble pairs may be produced in these double-stranded regions.

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.

Nussinov and Jacobson (1980) were the first to design a precise and efficient algorithm for predicting secondary structure.

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

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 ________

One of the first methods used to find tRNA genes was to search for sequences that are complementary and can fold into a knot like the three found in tRNAs.

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?

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

The dynamic programming method produces ____ structure with _____ score.

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

Which of the following is correct about MFOLD?

Which of the following about the RNAFold is incorrect?

The attractive interactions lead to _________ energy.

Four main subtypes of secondary structures can be identified. They are hairpin loops, bulge loops, interior loops, and multi-branch loops.

The ______ refers to a structure with two ends of a single-stranded region (loop) connecting a base-paired region (stem).

The __________ refers to two single-stranded regions on opposite strands connecting two adjacent base-paired segments.

Base pairing, in RNA, is A–G and U–C.

The object is to find a diagonal row of matches that goes from upper left to lower right.

In comparative approach to RNA structure prediction, the Foldalign program doesn’t use the covariation information.

In comparative approach to RNA structure prediction, algorithms that do not use pre-alignment, align multiple input sequences and infers a consensus structure.

In comparative approach to RNA structure prediction, Foldalign is a web-based only program for RNA alignment

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

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 ______

Ab initio methods are energetically least favorable.

______ molecules can simply be identified based on their sequence similarity with already-known sequences.

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

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.

If the base pair is adjacent to loops or bulges, the neighboring loops and bulges tend to ___________ the base-pair formation.

In ab initio approach, generally, when a base pairing is formed, the energy of the molecule is _________ because of attractive interactions between the two strands.

RNA secondary structure is composed primarily of triple-stranded RNA regions formed by folding the single-stranded molecule back twice on itself.

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

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?

In predicting RNA secondary structure, some simplifying assumptions are usually made, like the _____ structure is similar to the _____

A general theory for modeling strings of symbols, such as bases in DNA sequences, has been developed by linguists. There is a hierarchy of these so-called transformational grammars that deal with situations of increasing complexity.

If the centroid structure is different from the minimum free-energy structure, the centroid structure is often closer to the phylogenetic prediction and contains fewer base pairs, or fewer false-positive base pair predictions, than the minimum free-energy prediction.

The ILM program uses an iterative loop matching algorithm to maximize base pairs and allows pseudoknots to form by allowing base. pairs to be added or removed in successive rounds.

In comparative approach to RNA structure prediction, Dynalign is a ________ program.

In addition to the canonical base pairing, there often exists non-canonical base pairing such as _________ and ________ base paring.

Which of the following is incorrect about the RNA structure prediction?

The probabilistic model was used to identify small nucleolar (sno) RNAs in the yeast genome that methylate ribosomal RNA.

Which of the following is untrue about the Sfold algorithm?

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.

The use of SCFGs in RNA secondary structure production analysis is in fact very similar to that of the covariance model, with the grammatical productions resembling the nodes in the ordered binary tree.

The probability model mentioned above was a hybrid combination of HMMs and SCFGs trained on sno RNAs.

The dot matrix method and the dynamic programming method can be used in detecting self-complementary regions of a sequence.

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

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 ____

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

The dynamic programming method produces structure with _ score.

In predicting RNA secondary structure, some simplifying assumptions are usually made, like the _ structure is similar to the _

In addition to the canonical base pairing, there often exists non-canonical base pairing such as _ and base paring.