Which of the following is incorrect regarding pair wise sequence alignment?

The most fundamental process in this type of comparison is sequence alignment

It is an important first step toward structural and functional analysis of newly determined sequences

This is the process by which sequences are compared by searching for common character patterns and establishing residue-residue correspondence among related sequences

It is the process of aligning multiple sequences

Which of the following is untrue regarding dynamic programming algorithm?

The method compares every pair of characters in the two sequences and generates an alignment

The output alignment will include matched and mismatched characters and gaps in the two sequences that are positioned so that the number of matches between identical or related characters is the maximum possible

The dynamic programming algorithm provides a reliable computational method for aligning DNA and protein sequences

This doesn’t allow making evolutionary predictions on the basis of sequence alignments

The higher is the score in the alignment _________

or the less it resembles alignments in related proteins

the more significant is the alignment

or the less it resembles alignments in related proteins

the less significant is the alignment

the less it aligns with the related protein sequence

Which of the following doesn’t describe PAM matrices?

This family of matrices lists the likelihood of change from one amino acid to another in homologous protein sequences during evolution

There is presently no other type of scoring matrix that is based on such sound evolutionary principles as are these matrices

Even though they were originally based on a relatively small data set, the PAM matrices remain a useful tool for sequence alignment

It stands for Percent Altered Mutation

Which of the following is true regarding the assumptions in the method of constructing the Dayhoff scoring matrix?

it is assumed that each amino acid position is not equally mutable

it is assumed that each amino acid position is equally mutable

it is assumed that each amino acid position is not equally mutable

it is assumed that each amino acid position is not mutable at all

sites do not vary in their degree of mutability

Which of the following does not describe k-tuple methods?

k-tuple methods are best known for their implementation in the database search tools FASTA and the BLAST family

They are also known as words methods

They are basically heuristic methods to find local alignment

They are useful in small scale databases

Which of the following is true about Expectation Maximization (EM) method?

The final result is not sensitive to the initial alignment

The log odds scores of the PSSM are modified at the end of the process

The procedure stops prematurely if the scores reach convergence

The final result is not sensitive to the initial alignment

Local optimum is an advantage of EM method

In a dot matrix, two sequences to be compared are written in the _____________ of the matrix.

horizontal axis (one preceding another)

For what type of sequences Gibbs sampling is used?

Closely related sequences that share common motifs

Distinctly related sequences that share common motifs

Closely related sequences that share common motifs

Which of the following does not describe local alignment?

The substrings to be examined may be all of one or both sequences; if all of both are included then the local alignment is also global

A local alignment aligns a substring of the query sequence to a substring of the target sequence

A local alignment is defined by maximizing the alignment score, so that deleting a column from either end would reduce the score, and adding further columns at either end would also reduce the score

Local alignments have terminal gaps

The substrings to be examined may be all of one or both sequences; if all of both are included then the local alignment is also global

Which of the following does not describe local alignment algorithm?

First row and first column are set to 0 in initialization step

In traceback step, beginning is with the highest score, it ends when 0 is encountered

Which of the following is untrue about the PRSS program?

It holds one sequence in its original form and randomizes the order of residues in the other sequence.

It stands for Probability of Random Shuffles

It is a web-based program that can be used to evaluate the statistical significance of DNA or protein sequence alignment

It first aligns two sequences using the Needleman-Wunsch algorithm and calculates the score

It holds one sequence in its original form and randomizes the order of residues in the other sequence.

Which of the following does not describe BLOSUM matrices?

It stands for BLOcks SUbstitution Matrix

It was developed by Henikoff and Henikoff

The year it was developed was 1992

These matrices are logarithmic identity values

Which of the following does not describe global alignment algorithm?

It can use Needleman-Wunsch algorithm

It attempts to align every residue in every sequence

It is most useful when the aligning sequences are similar and of roughly the same size

It is useful when the aligning sequences are dissimilar

It can use Needleman-Wunsch algorithm

Which of the following is not the function of Short Linear Motifs?

Reversible cleavage of the peptide at the SLiM

Irreversible cleavage of the peptide at the SLiM

Reversible cleavage of the peptide at the SLiM

Moiety addition at targeted sites on SLiM

Structural modifications of the peptide backbone

Which of the following wrongly describes protein domains?

Defined as independently foldable units

They are made up of one secondary structure

Defined as independently foldable units

They are stable structures as compared to motifs

They are separated by linker regions

Which of the following is not a characteristic of exact matches in regular expression?

Searching a motif database using this approach results in either a match or non-match

There must be a strict match of sequence patterns

Any variations in the query sequence from the predefined patterns are not allowed

Provide more permissive matching by allowing more flexible matching of residues of similar biochemical properties

Searching a motif database using this approach results in either a match or non-match

151 + Mcqs in Statistical Significance Sequence Alignment in Bioinformatics Page 2 McqOptions

51.	Zhu (1998) have devised a computer program called the Bayes block aligner which in effect slides ____ sequences along each other to find the ______ ungapped regions or blocks.
A.	two, least scoring
B.	two, highest scoring
C.	multiple, highest scoring
D.	multiple, least scoring
Answer» C. multiple, highest scoring

53.	If the purpose is to calculate the probability of one event AND a second event, the odds scores for the events are _________
A.	added
B.	multiplied
C.	multiplied and added
D.	subtracted
Answer» C. multiplied and added

54.	The degree of sequence variation in the alignment reveals evolutionary relatedness of different sequences, whereas the conservation between sequences reflects the changes that have occurred during evolution in the form of substitutions, insertions, and deletions.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

56.	The assumption in this evolutionary model is that the amino acid substitutions observed over short periods of evolutionary history can be extrapolated to longer distances.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

62.	In the web-based program MEME, the computation is a _____ step procedure.
A.	one
B.	two
C.	three
D.	four
Answer» C. three

63.	Isolated dots that are not on the diagonal represent exact matches.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

64.	A multiple sequence alignment or a motif is often represented by a graphic representation called a ______
A.	logo
B.	motto
C.	algorithm
D.	algo
Answer» B. motto

65.	Dot plot of repeating elements would be small crosses on plot.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

66.	In a dot matrix, two sequences to be compared are written in the _____________ of the matrix.
A.	horizontal and vertical axes
B.	2 parallel horizontal axes
C.	2 parallel vertical axes
D.	horizontal axis (one preceding another)
Answer» B. 2 parallel horizontal axes

67.	In scoring matrices, for convenience, odds scores are converted to log odds scores.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

68.	Sometimes, it is also possible that two sequences have derived from a common ancestor, but may have diverged to such an extent that the common ancestral relationships are not recognizable at the sequence level.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

74.	Which of the following is not a software for dot plot analysis?
A.	SIMMI
B.	DOTLET
C.	DOTMATCHER
D.	LALIGN
Answer» B. DOTLET

75.	Which of the following is not a site on internet for alignment of sequence pairs?
A.	BLASTX
B.	BLASTN
C.	SIM
D.	BCM Search Launcher
Answer» B. BLASTN

77.	Sequence similarity can be quantified using ________ homology is a ______ statement.
A.	percentages, quantitative
B.	percentages, qualitative
C.	ratios, qualitative
D.	ratios, quantitative
Answer» C. ratios, qualitative

80.	_______ analyzed the distribution of scores among 100 vertebrate nucleic acid sequences and compared these scores with randomized sequences prepared in different ways.
A.	Lipman, in 1984
B.	Batalov, in 1964
C.	Waterman, in 1987
D.	Lipman, in 1967
Answer» B. Batalov, in 1964

69.	In a type of probability, analysis is to calculate the odds score for one event OR a second event, or of a series of events. In this case, the odds scores are _______
A.	multiplied
B.	subtracted
C.	added and multiplied
D.	added
Answer» E.

70.	If the two sequences share significant similarity, it is extremely ______ that the extensive similarity between the two sequences has been acquired randomly, meaning that the two sequences must have derived from a common evolutionary origin.
A.	unlikely
B.	possible
C.	likely
D.	relevant
Answer» B. possible

71.	When random or unrelated sequences are compared using a global alignment method, they can have ____________ reflecting the tendency of the global algorithm to match as many characters as possible.
A.	very low scores
B.	very high scores
C.	moderate scores
D.	low scores
Answer» C. moderate scores

72.	For what type of sequences Gibbs sampling is used?
A.	Closely related sequences
B.	Distinctly related sequences
C.	Distinctly related sequences that share common motifs
D.	Closely related sequences that share common motifs
Answer» D. Closely related sequences that share common motifs

73.	It is not known whether the Gumble distribution applies equally well to gapped alignments.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

78.	Which of the following does not describe local alignment algorithm?
A.	Score can be negative
B.	Negative score is set to 0
C.	First row and first column are set to 0 in initialization step
D.	In traceback step, beginning is with the highest score, it ends when 0 is encountered
Answer» B. Negative score is set to 0

79.	The more conserved amino acids in similar proteins from different species are ones that play an essential role in structure and function and the less conserved are in sites that can vary without having a significant effect on function.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

82.	The major disadvantage of the PRSS program is that it doesn’t allow partial shuffling.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

83.	When did Smith–Waterman first describe the algorithm for local alignment?
A.	1950
B.	1970
C.	1981
D.	1925
Answer» D. 1925

84.	Who were the inventors of dot plot method?
A.	Smith-Waterman
B.	Margaret Preston
C.	Gibbs and McIntyre
D.	Needleman-Wunsch
Answer» D. Needleman-Wunsch

Explore topic-wise MCQs in Bioinformatics.

Zhu (1998) have devised a computer program called the Bayes block aligner which in effect slides ____ sequences along each other to find the ______ ungapped regions or blocks.

Which of the following is incorrect regarding pair wise sequence alignment?

If the purpose is to calculate the probability of one event AND a second event, the odds scores for the events are _________

The degree of sequence variation in the alignment reveals evolutionary relatedness of different sequences, whereas the conservation between sequences reflects the changes that have occurred during evolution in the form of substitutions, insertions, and deletions.

Which of the following is untrue regarding dynamic programming algorithm?

The assumption in this evolutionary model is that the amino acid substitutions observed over short periods of evolutionary history can be extrapolated to longer distances.

The higher is the score in the alignment _________

Which of the following doesn’t describe PAM matrices?

Which of the following is true regarding the assumptions in the method of constructing the Dayhoff scoring matrix?

Which of the following does not describe k-tuple methods?

Which of the following is true about Expectation Maximization (EM) method?

In the web-based program MEME, the computation is a _____ step procedure.

Isolated dots that are not on the diagonal represent exact matches.

A multiple sequence alignment or a motif is often represented by a graphic representation called a ______

Dot plot of repeating elements would be small crosses on plot.

In a dot matrix, two sequences to be compared are written in the _____________ of the matrix.

In scoring matrices, for convenience, odds scores are converted to log odds scores.

Sometimes, it is also possible that two sequences have derived from a common ancestor, but may have diverged to such an extent that the common ancestral relationships are not recognizable at the sequence level.

In a type of probability, analysis is to calculate the odds score for one event OR a second event, or of a series of events. In this case, the odds scores are _______

If the two sequences share significant similarity, it is extremely ______ that the extensive similarity between the two sequences has been acquired randomly, meaning that the two sequences must have derived from a common evolutionary origin.

When random or unrelated sequences are compared using a global alignment method, they can have ____________ reflecting the tendency of the global algorithm to match as many characters as possible.

For what type of sequences Gibbs sampling is used?

It is not known whether the Gumble distribution applies equally well to gapped alignments.

Which of the following is not a software for dot plot analysis?

Which of the following is not a site on internet for alignment of sequence pairs?

Which of the following does not describe local alignment?

Sequence similarity can be quantified using ________ homology is a ______ statement.

Which of the following does not describe local alignment algorithm?

The more conserved amino acids in similar proteins from different species are ones that play an essential role in structure and function and the less conserved are in sites that can vary without having a significant effect on function.

_______ analyzed the distribution of scores among 100 vertebrate nucleic acid sequences and compared these scores with randomized sequences prepared in different ways.

Which of the following is untrue about the PRSS program?

The major disadvantage of the PRSS program is that it doesn’t allow partial shuffling.

When did Smith–Waterman first describe the algorithm for local alignment?

Who were the inventors of dot plot method?

Unlike the commonly used methods for aligning a pair of sequences, the Bayesian method _______ using a particular scoring matrix or designated gap penalties.

A gap opening penalty for any gap (g) and a gap extension penalty for each element in the gap (r) are most often used, to give a total gap score wx, according to the equation ______

By whom and when were the Bayesian methods applied first?

Alignment algorithms, both global and local, are fundamentally similar and only differ in the optimization strategy used in aligning similar residues.

Which of the following does not describe BLOSUM matrices?

Dayhoff PAM matrices, are based on an evolutionary model of protein change, whereas, BLOSUM matrices, are designed to identify members of the same family.

Which of the following does not describe global alignment algorithm?

In local alignment, the two sequences to be aligned cannot be of unequal lengths.

Among the following which one is not the approach to the local alignment?

Who suggested that the global alignment scores between unrelated protein sequences followed the extreme value distribution, similar to local alignment scores? And when?

The protein structural motif domain- helix loop helix are contained by all of the following except ________

In the zinc finger, which residues in this sequence motif form ligands to a zinc ion?

Which of the following is not the function of Short Linear Motifs?

Which of the following wrongly describes protein domains?

Motifs that can form α/β horseshoes conformation are rich with which protein residue?

Which of the following is not a characteristic of exact matches in regular expression?

Zhu (1998) have devised a computer program called the Bayes block aligner which in effect slides sequences along each other to find the __ ungapped regions or blocks.

Sequence similarity can be quantified using __ homology is a statement.

85.	Unlike the commonly used methods for aligning a pair of sequences, the Bayesian method _______ using a particular scoring matrix or designated gap penalties.
A.	does not depend on
B.	depends on
C.	is based on
D.	involves
Answer» B. depends on

86.	A gap opening penalty for any gap (g) and a gap extension penalty for each element in the gap (r) are most often used, to give a total gap score wx, according to the equation ______
A.	wx – rx = -g
B.	wx = g – rx
C.	wx = g + rx
D.	wx + g + rx = 0
Answer» D. wx + g + rx = 0

87.	By whom and when were the Bayesian methods applied first?
A.	Smith-Waterman, 1981
B.	Agarwal and States, 1996
C.	Smith-Waterman, 1996
D.	Agarwal and States, 1981
Answer» C. Smith-Waterman, 1996

93.	Among the following which one is not the approach to the local alignment?
A.	Smith-Waterman algorithm
B.	K-tuple method
C.	Words method
D.	Needleman-Wunsch algorithm
Answer» E.

94.	Who suggested that the global alignment scores between unrelated protein sequences followed the extreme value distribution, similar to local alignment scores? And when?
A.	Abagyan and Batalov, in 1981
B.	Chvátal and Lipman, in 1984
C.	Abagyan and Batalov, in 1997
D.	Chvátal and Sankoff, in 1995
Answer» D. Chvátal and Sankoff, in 1995

95.	The protein structural motif domain- helix loop helix are contained by all of the following except ________
A.	Scleraxis
B.	Neurogenins
C.	Transcription Factor 4
D.	Leucine zipper
Answer» E.

96.	In the zinc finger, which residues in this sequence motif form ligands to a zinc ion?
A.	Cysteine and histidine
B.	Cysteine and arginine
C.	Histidine and proline
D.	Histidine and arginine
Answer» B. Cysteine and arginine

99.	Motifs that can form α/β horseshoes conformation are rich with which protein residue?
A.	Proline
B.	Arginine
C.	Valine
D.	Leucine
Answer» E.

100.	Which of the following is not a characteristic of exact matches in regular expression?
A.	There must be a strict match of sequence patterns
B.	Any variations in the query sequence from the predefined patterns are not allowed
C.	Provide more permissive matching by allowing more flexible matching of residues of similar biochemical properties
D.	Searching a motif database using this approach results in either a match or non-match
Answer» D. Searching a motif database using this approach results in either a match or non-match