Which of the following is incorrect regarding sequence homology?

It is an important concept in sequence analysis

Two sequences can homologous relationship even if have do not have common origin

It is an important concept in sequence analysis

When two sequences are descended from a common evolutionary origin, they are said to have a homologous relationship

When two sequences are descended from a common evolutionary origin, they are said to share homology

Which of the following is not a description of dynamic programming algorithm?

A method that can take gaps into account

A method that requires a manageable number of comparisons

This method doesn’t provide an optimal (highest scoring) alignment

Which of the following are not related to Needleman-Wunsch alignment algorithm?

Global alignment programs use this algorithm

The output is a positive number

Small changes in the scoring system can produce a different alignment

Changes in the scoring system can produce the same alignment

Which of the following feature of Bayesian methods is the disadvantage of it?

A length and distance that gives the highest overall probability may be determined

They are used to calculate evolutionary distance

Computationally Bayesian methods are better

A specific mutational model is required

The statistical analysis of alignment scores is much better understood for ________ than for _______

global alignments, any other alignment method

global alignments, local alignments

local alignments, global alignments

global alignments, any other alignment method

Needleman-Wunsch alignment, Smith-Waterman alignment

Dayhoff, 1978- 1983, devised a second method for testing the relatedness of two protein sequences that can accommodate some local variation. Where this method is useful?

For finding repeated regions within a sequence

For finding similar regions that are in a different order in two sequences

For finding small conserved region such as an active site

For finding huge regions within sequences

The matrices PAM250 and BLOSUM62 contain _______

neither positive nor negative values, just the percentage

For palindromic sequences, what is the structure of the dot plot?

2 intersecting diagonal lines at the midpoint

Which of the following does not describe BLAST?

It stands for Basic Local Alignment Search Tool

It uses word matching like FASTA

It is one of the tools of the NCBI

Even if no words are similar, there is an alignment to be considered

For significantly aligning sequences what is the resulting structure on the plot?

A diagonal and lines parallel to diagonal

Which of the following is incorrect about evolution?

The macromolecules can be considered molecular fossils that encode the history of millions of years of evolution

The building blocks of these biological macromolecules, nucleotide bases, and amino acids form linear sequences that determine the primary structure of the molecules

DNA and proteins are products of evolution

The molecular sequences barely undergo changes

A length and distance that gives the highest overall probability may then be determined. Such alignments are initially found using ________

a particular scoring matrix only

an alignment algorithm and a particular scoring matrix

Which of the following is true for EMBOSS Dottup?

Doesn’t allow you to specify window size

Allows you to specify threshold

Doesn’t allow you to specify threshold

Doesn’t allow you to specify window size

If all cells in the window are identity, it colors in some specific cells in the window

Gaps are added to the alignment because it ______

increases the matching of or dissimilar amino acids at subsequent portions in the alignment

increases the matching of identical amino acids at subsequent portions in the alignment

increases the matching of or dissimilar amino acids at subsequent portions in the alignment

enhances the area of the sequences

Which of the following is untrue regarding BLAST and FASTA?

BLAST has limited choices of databases

FASTA is more sensitive for DNA-DNA comparisons

Local alignments are more used when _____________

Dissimilar sequences are suspected to contain regions of similarity

There are totally similar and equal length sequences

Dissimilar sequences are suspected to contain regions of similarity

Similar sequence motif with larger sequence context

Partially similar, different length and conserved region containing sequences

On analysis of the alignment scores of random sequences will reveal that the scores follow a different distribution than the normal distribution called the _________

Gumbel equal value distribution

Gumbel extreme value distribution

MEME stands for _____________

Multiple Expectation Maximization for Motif Extraction

Multiple Expectation Maximization for Motif Elicitation

Multiple Expectation Maximization for Motif Extraction

Mega Expectation Maximization for Motif Elicitation

Micro Expectation Maximization for Motif Extraction

Which of the following is untrue about dot plot method and its applications?

The method can be used in identifying nucleic acid secondary structures through detecting self-complementarity of a sequence

This method gives a direct visual statement of the relationship between two sequences

One of its advantages is the identification of sequence repeat regions based on the presence of parallel diagonals of the same size vertically or horizontally in the matrix

It is not useful in identifying chromosomal repeats

The method can be used in identifying nucleic acid secondary structures through detecting self-complementarity of a sequence

Which of the following is untrue regarding the gap penalty used in dynamic programming?

The gap score defines a penalty given to alignment when we have insertion or deletion

Gap penalty is subtracted for each gap that has been introduced

Gap penalty is added for each gap that has been introduced

The gap score defines a penalty given to alignment when we have insertion or deletion

Gap open and gap extension has been introduced when there are continuous gaps (five or more)

Which of the following is untrue about the modification of PAM matrices?

These modifications were included as the default matrices for the GCG sequence alignment programs in versions 8 and earlier and are optional in later versions

At one time, the PAM250 scoring matrix was modified in an attempt to improve the alignment obtained

All scores for matching a particular amino acid were normalized to the same mean and standard deviation, and all amino acid identities were given the same score to provide an equal contribution for each amino acid in a sequence alignment

These modifications were included as the default matrices for the GCG sequence alignment programs in versions 8 and earlier and are optional in later versions

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

It is used to find hidden motifs

The method works by first making a random or guessed alignment of the sequences to generate a trial PSSM

The trial PSSM is used to compare with each sequence individually

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

151 + Mcqs in Statistical Significance Sequence Alignment in Bioinformatics Page 1 McqOptions

1.	Shorter sequences require higher cutoffs for inferring homologous relationships than longer sequences.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

3.	Use of the dynamic programming method requires a scoring system for the comparison of symbol pairs, and a scheme for GAP penalties.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

4.	Another difficulty in Bayesian methods is deciding on the length of sequence that was duplicated.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

5.	When was the dot plot method, first described?
A.	1959
B.	1966
C.	1970
D.	1982
Answer» D. 1982

6.	The GCG alignment programs have a RANDOMIZATION option, which shuffles the second sequence and calculates similarity scores between the unshuffled sequence and each of the shuffled copies.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

7.	Which of the following is not a description of dynamic programming algorithm?
A.	A method of sequence alignment
B.	A method that can take gaps into account
C.	A method that requires a manageable number of comparisons
D.	This method doesn’t provide an optimal (highest scoring) alignment
Answer» E.

11.	Sequence similarity and sequence identity are synonymous for nucleotide sequences and protein sequences as well.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

12.	If the random sequences were prepared in a way that maintained the local base composition by producing them from overlapping fragments of sequence, the distribution of scores has a _______ standard deviation that is closer to the distribution of the natural sequences.
A.	lowest
B.	higher
C.	lower
D.	moderate
Answer» D. moderate

14.	The matrices PAM250 and BLOSUM62 contain _______
A.	positive and negative values
B.	positive values only
C.	negative values only
D.	neither positive nor negative values, just the percentage
Answer» B. positive values only

15.	A sequence can be aligned with itself to identify internal repeat elements.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

16.	Self complementarity of DNA sequences cannot be identified using a dot plot.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

19.	When the two sequences have substantial regions of similarity, many dots line up to form contiguous _______ lines.
A.	crossings on
B.	horizontal
C.	diagonal
D.	vertical
Answer» D. vertical

20.	Vertical frame shifts show ______ while the horizontal ones show _______
A.	insertion, insertion
B.	insertion, deletion
C.	deletion, deletion
D.	deletion, insertion
Answer» C. deletion, deletion

22.	A problem exists when comparing _____ sequences using the dot matrix method, namely, the _______
A.	small, amplification
B.	large, amplification
C.	small, high noise level
D.	large, high noise level
Answer» E.

23.	_______ is an interactive program for generating sequence logos.
A.	EMBOSS
B.	WebLogo
C.	LOGOLY
D.	BLAST
Answer» C. LOGOLY

17.	For palindromic sequences, what is the structure of the dot plot?
A.	2 intersecting diagonal lines at the midpoint
B.	One diagonal
C.	Two parallel diagonals
D.	No diagonal
Answer» B. One diagonal

18.	In the GCG and FASTA program suites, the scoring matrix itself is formatted in a way that includes default ______
A.	gap additions
B.	alignment scores
C.	score penalties
D.	gap penalties
Answer» E.

21.	The presence of evolutionary traces is because some of the residues that perform key functional and structural roles tend to be preserved by natural selection; other residues that may be less crucial for structure and function tend to mutate more frequently.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

24.	The softwares for dot plot analysis perform several tasks. Which one of them is not performed by them?
A.	Gap open penalty
B.	Gap extend penalty
C.	Expectation threshold
D.	Change or mutate residues
Answer» E.

26.	For significantly aligning sequences what is the resulting structure on the plot?
A.	Intercrossing lines
B.	Crosses everywhere
C.	Vertical lines
D.	A diagonal and lines parallel to diagonal
Answer» E.

28.	Conserved positions have _____ residues and bigger symbols.
A.	fewer
B.	more
C.	maximum
D.	minimum
Answer» B. more

29.	A length and distance that gives the highest overall probability may then be determined. Such alignments are initially found using ________
A.	a particular scoring matrix only
B.	an alignment algorithm only
C.	an alignment algorithm and a particular scoring matrix
D.	dot method
Answer» D. dot method

32.	Gibbs is a web-based program that uses the Gibbs sampling approach to look for _____ gap-free segments for either DNA or protein sequences.
A.	short, partially conserved
B.	long, partially conserved
C.	long, conserved
D.	short, not conserved
Answer» B. long, partially conserved

33.	Which of the following is untrue regarding BLAST and FASTA?
A.	FASTA is faster than BLAST
B.	FASTA is the most accurate
C.	BLAST has limited choices of databases
D.	FASTA is more sensitive for DNA-DNA comparisons
Answer» B. FASTA is the most accurate

34.	The overall goal of pair wise sequence alignment is to find the best pairing of two sequences, such that there is maximum correspondence among residues.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Explore topic-wise MCQs in Bioinformatics.

Shorter sequences require higher cutoffs for inferring homologous relationships than longer sequences.

Which of the following is incorrect regarding sequence homology?

Use of the dynamic programming method requires a scoring system for the comparison of symbol pairs, and a scheme for GAP penalties.

Another difficulty in Bayesian methods is deciding on the length of sequence that was duplicated.

When was the dot plot method, first described?

The GCG alignment programs have a RANDOMIZATION option, which shuffles the second sequence and calculates similarity scores between the unshuffled sequence and each of the shuffled copies.

Which of the following is not a description of dynamic programming algorithm?

Which of the following are not related to Needleman-Wunsch alignment algorithm?

Which of the following feature of Bayesian methods is the disadvantage of it?

The statistical analysis of alignment scores is much better understood for ________ than for _______

Sequence similarity and sequence identity are synonymous for nucleotide sequences and protein sequences as well.

If the random sequences were prepared in a way that maintained the local base composition by producing them from overlapping fragments of sequence, the distribution of scores has a _______ standard deviation that is closer to the distribution of the natural sequences.

Dayhoff, 1978- 1983, devised a second method for testing the relatedness of two protein sequences that can accommodate some local variation. Where this method is useful?

The matrices PAM250 and BLOSUM62 contain _______

A sequence can be aligned with itself to identify internal repeat elements.

Self complementarity of DNA sequences cannot be identified using a dot plot.

For palindromic sequences, what is the structure of the dot plot?

In the GCG and FASTA program suites, the scoring matrix itself is formatted in a way that includes default ______

When the two sequences have substantial regions of similarity, many dots line up to form contiguous _______ lines.

Vertical frame shifts show ______ while the horizontal ones show _______

The presence of evolutionary traces is because some of the residues that perform key functional and structural roles tend to be preserved by natural selection; other residues that may be less crucial for structure and function tend to mutate more frequently.

A problem exists when comparing _____ sequences using the dot matrix method, namely, the _______

_______ is an interactive program for generating sequence logos.

The softwares for dot plot analysis perform several tasks. Which one of them is not performed by them?

Which of the following does not describe BLAST?

For significantly aligning sequences what is the resulting structure on the plot?

Which of the following is incorrect about evolution?

Conserved positions have _____ residues and bigger symbols.

A length and distance that gives the highest overall probability may then be determined. Such alignments are initially found using ________

Which of the following is true for EMBOSS Dottup?

Gaps are added to the alignment because it ______

Gibbs is a web-based program that uses the Gibbs sampling approach to look for _____ gap-free segments for either DNA or protein sequences.

Which of the following is untrue regarding BLAST and FASTA?

The overall goal of pair wise sequence alignment is to find the best pairing of two sequences, such that there is maximum correspondence among residues.

In Bayesian methods, difficulty with making estimations is that the estimate depends on the following Assumption. (Assumption – The mutation rate in sequences has been constant with time and that the rate of mutation of all nucleotides is the same.)

The overall height of a logo position reflects how conserved the position is, and the _____ of each letter in a position reflects the _______ of the residue in the alignment.

Local alignments are more used when _____________

On analysis of the alignment scores of random sequences will reveal that the scores follow a different distribution than the normal distribution called the _________

MEME stands for _____________

With the application of Bayesian methods, the most probable repeat length and evolutionary time since the repeat was formed may be derived.

If the selected window size is too long, sensitivity of the alignment is lost.

Waterman, in1989, provided a set of means and standard deviations of global alignment scores between random DNA sequences, using mismatch and gap penalties that produce a linear increase in score with _______ a distinguishing feature of global alignments.

After the derivation, the outputs of the dynamic programming are the ratios are called even scores.

Which of the following is untrue about dot plot method and its applications?

In case of the varying alignment, penalizing gaps heavily might occur. Then the best scoring local alignment between the sequences will be one that optimizes the score between matches and mismatches, without any gaps.

Which of the following is untrue regarding the gap penalty used in dynamic programming?

A feature of the dynamic programming algorithm is that the alignments obtained depend on the choice of a scoring system for comparing character pairs and penalty scores for gaps.

The Dayhoff model of protein evolution is not a Markov process.

Which of the following is untrue about the modification of PAM matrices?

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

The statistical analysis of alignment scores is much better understood for __ than for _

Vertical frame shifts show while the horizontal ones show _

A problem exists when comparing _ sequences using the dot matrix method, namely, the ___

The overall height of a logo position reflects how conserved the position is, and the _ of each letter in a position reflects the ___ of the residue in the alignment.

36.	The overall height of a logo position reflects how conserved the position is, and the _____ of each letter in a position reflects the _______ of the residue in the alignment.
A.	height, relative frequency
B.	width, relative frequency
C.	height, amplitude
D.	width, amplitude
Answer» B. width, relative frequency

42.	Waterman, in1989, provided a set of means and standard deviations of global alignment scores between random DNA sequences, using mismatch and gap penalties that produce a linear increase in score with _______ a distinguishing feature of global alignments.
A.	alignment score
B.	sequence score
C.	sequence length
D.	scoring system
Answer» D. scoring system