Which of the following is untrue about Vienna RNA Websuite?

It introduced the Wuchty algorithm, developed applications of the McCaskill algorithm

It also offers a wide variety of algorithms and functions

The Wuchty algorithm generates a small but complete set of suboptimal structures

The Wuchty algorithm computes some possible tertiary structures within a narrow free-energy range

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

The sequence is listed across the top and down the side of the page, and G/C, A/U, and G/U base pairs are scored

Every base is first compared to every other base by a type of analysis very similar to the dot matrix analysis

A row of matches in the RNA matrix indicates a succession of complementary nucleotides that can potentially form a double-stranded region

A row of matches in the RNA matrix indicates a failure of complementary nucleotides that can potentially form a double-stranded region

The sequence is listed across the top and down the side of the page, and G/C, A/U, and G/U base pairs are scored

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?

represents in an unfiltered dot plot

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

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

represents in an unfiltered dot plot

represents the number of base pairs

In comparative approach to RNA structure prediction, in Dynalign program–by comparing _________ from each sequence, a ______ structure common to both sequences is selected that serves as the basis for sequence alignment.

single structure, lowest energy

multiple alternative structures, lowest energy

single structure, lowest energy

single structure, highest energy

multiple alternative structures, highest energy

Which of the following is untrue regarding RNA structure?

RNA structure 4.6 is a Windows implementation of the Zuker algorithm

It includes additional options for other folding algorithms and incorporation of experimental data

The authors of RNA structure collaborate very closely with the Turner laboratory and keep the most up-to-date thermodynamic parameters

The OligoWalk program cannot be used for siRNA design

If prediction accuracy can be represented using a ______ the ______ programs score roughly 20% to 60% depending on the length of the sequences.

multiple parameter, comparative–based

multiple parameter, ab initio–based

single parameter, ab initio–based

multiple parameter, comparative–based

single parameter, comparative–based

The type of algorithm that _____ predefined alignment is ______ for reasonably conserved sequences.

doesn’t require, more successful

doesn’t require, relatively successful

requires, relatively successful

Which of the following is true about the RNAalifold?

Dynamic programming is not involved

Minimum free energy method is not used

Only minimum free energy is used

Covariation information is taken into consideration

RNA structures can be experimentally determined using _____

X-ray crystallography techniques only

X-ray crystallography or NMR techniques

97 + Mcqs in Rna Secondary Structure Prediction Methods in Bioinformatics Page 2 McqOptions

51.	The program may be instructed to find structures within a certain percentage of the minimum free energy.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

52.	Which of the following is untrue about Vienna RNA Websuite?
A.	It introduced the Wuchty algorithm, developed applications of the McCaskill algorithm
B.	It also offers a wide variety of algorithms and functions
C.	The Wuchty algorithm generates a small but complete set of suboptimal structures
D.	The Wuchty algorithm computes some possible tertiary structures within a narrow free-energy range
Answer» E.

Discussion

53.	Which of the following is incorrect about the prediction of RNA secondary structure?
A.	Every base is first compared to every other base by a type of analysis very similar to the dot matrix analysis
B.	A row of matches in the RNA matrix indicates a succession of complementary nucleotides that can potentially form a double-stranded region
C.	A row of matches in the RNA matrix indicates a failure of complementary nucleotides that can potentially form a double-stranded region
D.	The sequence is listed across the top and down the side of the page, and G/C, A/U, and G/U base pairs are scored
Answer» D. The sequence is listed across the top and down the side of the page, and G/C, A/U, and G/U base pairs are scored

Discussion

54.	The sequence is listed down the first column of base comparisons’ table and free energy calculations’ table in the 5’→3’ orientation.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

55.	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
Answer» C. represents in an unfiltered dot plot

Discussion

56.	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
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

57.	Rigorously evaluating the performance of RNA prediction programs has traditionally been hindered by the dearth of three-dimensional structural information for RNA.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

58.	For _________ RNA sequences, such as tRNA, some programs may be able to produce _________% accuracy.
A.	small, 70
B.	small, 40
C.	large, 90
D.	large, 75
Answer» B. small, 40

Discussion

59.	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
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

60.	The application of SCFGs to RNA secondary structure analysis is very similar in form to the probabilistic covariance models.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

61.	Fichant and Burks (1991) described a program, tRNAscan, that searches a genomic sequence with a sliding window searching simultaneously for matches to a set of invariant bases and conserved self-complementary regions in tRNAs with an accuracy of 97.5%.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

62.	In comparative approach to RNA structure prediction, in Dynalign program–by comparing _________ from each sequence, a ______ structure common to both sequences is selected that serves as the basis for sequence alignment.
A.	multiple alternative structures, lowest energy
B.	single structure, lowest energy
C.	single structure, highest energy
D.	multiple alternative structures, highest energy
Answer» B. single structure, lowest energy

Discussion

63.	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
Answer» E.

Discussion

64.	The scoring scheme based on the combined stabilizing and destabilizing interactions forms the foundation of the ab initio RNA secondary structure prediction method.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

65.	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
Answer» D. multiple, small

Discussion

66.	Based on recent benchmark comparisons, the comparative-type algorithms can reach an accuracy range of 20% to 80%.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

67.	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
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

68.	The increase depends on the type and length of loop that is introduced by the non-complementary base pair, whether internal loop, bulge loop, or hairpin loop.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

69.	Which of the following is untrue regarding RNA structure?
A.	RNA structure 4.6 is a Windows implementation of the Zuker algorithm
B.	It includes additional options for other folding algorithms and incorporation of experimental data
C.	The authors of RNA structure collaborate very closely with the Turner laboratory and keep the most up-to-date thermodynamic parameters
D.	The OligoWalk program cannot be used for siRNA design
Answer» E.

Discussion

70.	If prediction accuracy can be represented using a ______ the ______ programs score roughly 20% to 60% depending on the length of the sequences.
A.	multiple parameter, ab initio–based
B.	single parameter, ab initio–based
C.	multiple parameter, comparative–based
D.	single parameter, comparative–based
Answer» C. multiple parameter, comparative–based

Discussion

71.	At present, there are essentially two types of method of RNA structure prediction. One is the minimum free energy approach and the Second one is a comparative approach.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

72.	The pre-alignment independent programs fare __________ for predicting long sequences.
A.	slight better
B.	much better
C.	a bit worse
D.	much worse
Answer» E.

Discussion

73.	___________ of covariation can be ___________ to the RNA structure and functions.
A.	Any lack, deleterious
B.	Any lack, benign
C.	Any abundance, deleterious
D.	Any inadequacy, advantageous
Answer» B. Any lack, benign

Discussion

74.	An aspect of the comparative method is to select a __________ structure through consensus drawing.
A.	relatively distinct
B.	remote
C.	common
D.	least abundant
Answer» D. least abundant

Discussion

75.	The comparative approach uses basic RNA structure based predictions to infer a consensus structure.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

76.	In ab initio methods for RNA structure prediction, the prediction results from RNAfold are not always guaranteed to be better than those predicted by Mfold.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

77.	To distinguish the conserved secondary structure among multiple related RNA sequences, a concept of “covariation” is used.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

78.	The predefined alignment requiring method also depends on the quality of the input alignment. If there ___ errors in the alignment, covariation signals ____ detected.
A.	are, will be
B.	are, will not be
C.	are not, will not be
D.	are not, possibly will not be
Answer» C. are not, will not be

Discussion

79.	The type of algorithm that _____ predefined alignment is ______ for reasonably conserved sequences.
A.	doesn’t require, more successful
B.	requires, less successful
C.	doesn’t require, relatively successful
D.	requires, relatively successful
Answer» E.

Discussion

80.	Which of the following is true about the RNAalifold?
A.	Dynamic programming is not involved
B.	Minimum free energy method is not used
C.	Only minimum free energy is used
D.	Covariation information is taken into consideration
Answer» E.

Discussion

81.	The comparative-based algorithms can be further divided into two categories based on the type of input data.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

82.	The type of algorithm that requires predefined alignment, requires the user to provide _______ alignment as input.
A.	not necessarily an alignment
B.	multiple only
C.	pairwise or multiple
D.	pair wise only
Answer» D. pair wise only

Discussion

83.	Which of the following is not a base of RNA?
A.	Thymine (T)
B.	Adenine (A)
C.	Cytosine (C)
D.	Guanine (G)
Answer» B. Adenine (A)

Discussion

84.	RNA structures can be experimentally determined using _____
A.	X-ray crystallography techniques only
B.	NMR techniques only
C.	X-ray crystallography or NMR techniques
D.	Gel electrophoresis
Answer» D. Gel electrophoresis

Discussion

85.	Which of the following is not a form of RNA?
A.	mRNA
B.	tRNA
C.	qRNA
D.	rRNA
Answer» D. rRNA

Discussion

86.	Unlike DNA, which is mainly double stranded, RNA is double stranded, although an RNA molecule can self-hybridize at certain regions to form partial double-stranded structures.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

87.	Structures are not much important when it comes to the study of the functions.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

88.	AB_INITIO_METHODS_ARE_ENERGETICALLY_LEAST_FAVORABLE.?$
A.	True
B.	False
Answer» C.

Discussion

89.	The_dot_matrix_method_and_the_dynamic_programming_method_can_be_used_in_detecting_self-complementary_regions_of_a_sequence.$
A.	True
B.	False
Answer» B. False

Discussion

90.	The scoring scheme based on the combined stabilizing and destabilizing interactions forms the foundation of the ab initio RNA secondary structure prediction method?
A.	True
B.	False
Answer» B. False

Discussion

91.	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

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

Discussion

93.	The energy necessary to form individual base pairs is not quite affected by adjacent base pairs.
A.	True
B.	False
Answer» C.

Discussion

94.	In ab initio methods, free energy can be calculated based on parameters empirically derived for small molecules.
A.	True
B.	False
Answer» B. False

Discussion

95.	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

96.	Ab initio approach makes structural predictions based on ______
A.	a single RNA sequence
B.	comparing RNA sequences
C.	evolutionary basis
D.	pure phylogenetics
Answer» B. comparing RNA sequences

Discussion

97.	At present, there are essentially two types of method of RNA structure prediction.
A.
B.	True
Answer» B. True

Discussion

Explore topic-wise MCQs in Bioinformatics.

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

Which of the following is untrue about Vienna RNA Websuite?

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

The sequence is listed down the first column of base comparisons’ table and free energy calculations’ table in the 5’→3’ orientation.

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?

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.

Rigorously evaluating the performance of RNA prediction programs has traditionally been hindered by the dearth of three-dimensional structural information for RNA.

For _________ RNA sequences, such as tRNA, some programs may be able to produce _________% accuracy.

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.

The application of SCFGs to RNA secondary structure analysis is very similar in form to the probabilistic covariance models.

Fichant and Burks (1991) described a program, tRNAscan, that searches a genomic sequence with a sliding window searching simultaneously for matches to a set of invariant bases and conserved self-complementary regions in tRNAs with an accuracy of 97.5%.

In comparative approach to RNA structure prediction, in Dynalign program–by comparing _________ from each sequence, a ______ structure common to both sequences is selected that serves as the basis for sequence alignment.

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

The scoring scheme based on the combined stabilizing and destabilizing interactions forms the foundation of the ab initio RNA secondary structure prediction method.

In dynamic programming, in ab initio methods, the use of a dot plot can be effective in finding a ____ secondary structure in a ________ molecule.

Based on recent benchmark comparisons, the comparative-type algorithms can reach an accuracy range of 20% to 80%.

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.

The increase depends on the type and length of loop that is introduced by the non-complementary base pair, whether internal loop, bulge loop, or hairpin loop.

Which of the following is untrue regarding RNA structure?

If prediction accuracy can be represented using a ______ the ______ programs score roughly 20% to 60% depending on the length of the sequences.

At present, there are essentially two types of method of RNA structure prediction. One is the minimum free energy approach and the Second one is a comparative approach.

The pre-alignment independent programs fare __________ for predicting long sequences.

___________ of covariation can be ___________ to the RNA structure and functions.

An aspect of the comparative method is to select a __________ structure through consensus drawing.

The comparative approach uses basic RNA structure based predictions to infer a consensus structure.

In ab initio methods for RNA structure prediction, the prediction results from RNAfold are not always guaranteed to be better than those predicted by Mfold.

To distinguish the conserved secondary structure among multiple related RNA sequences, a concept of “covariation” is used.

The predefined alignment requiring method also depends on the quality of the input alignment. If there ___ errors in the alignment, covariation signals ____ detected.

The type of algorithm that _____ predefined alignment is ______ for reasonably conserved sequences.

Which of the following is true about the RNAalifold?

The comparative-based algorithms can be further divided into two categories based on the type of input data.

The type of algorithm that requires predefined alignment, requires the user to provide _______ alignment as input.

Which of the following is not a base of RNA?

RNA structures can be experimentally determined using _____

Which of the following is not a form of RNA?

Unlike DNA, which is mainly double stranded, RNA is double stranded, although an RNA molecule can self-hybridize at certain regions to form partial double-stranded structures.

Structures are not much important when it comes to the study of the functions.

AB_INITIO_METHODS_ARE_ENERGETICALLY_LEAST_FAVORABLE.?$

The_dot_matrix_method_and_the_dynamic_programming_method_can_be_used_in_detecting_self-complementary_regions_of_a_sequence.$

The scoring scheme based on the combined stabilizing and destabilizing interactions forms the foundation of the ab initio RNA secondary structure prediction method?

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

The attractive interactions lead to ____ energy.

The energy necessary to form individual base pairs is not quite affected by adjacent base pairs.

In ab initio methods, free energy can be calculated based on parameters empirically derived for small molecules.

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.

Ab initio approach makes structural predictions based on ______

At present, there are essentially two types of method of RNA structure prediction.

For _ RNA sequences, such as tRNA, some programs may be able to produce _% accuracy.

In comparative approach to RNA structure prediction, in Dynalign program–by comparing ___ from each sequence, a structure common to both sequences is selected that serves as the basis for sequence alignment.

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

In dynamic programming, in ab initio methods, the use of a dot plot can be effective in finding a secondary structure in a ____ molecule.

If prediction accuracy can be represented using a the programs score roughly 20% to 60% depending on the length of the sequences.

_ of covariation can be _ to the RNA structure and functions.

The predefined alignment requiring method also depends on the quality of the input alignment. If there _ errors in the alignment, covariation signals __ detected.

The type of algorithm that _ predefined alignment is __ for reasonably conserved sequences.