Which of the following is untrue regarding Expectation Maximization algorithm?

An initial guess is made as to the location and size of the site of interest in each of the sequences, and these parts of the sequence are aligned

The alignment provides an estimate of the base or amino acid composition of each column in the site

The column-by-column composition of the site already available is used to estimate the probability of finding the site at any position in each of the sequences

The row-by-column composition of the site already available is used to estimate the probability

Which of the following about the Gibbs sampler is untrue?

It searches for the statistically most probable motifs

It is a statistical method for finding motifs in sequences

It is dissimilar to the principle of the EM method

It searches for the statistically most probable motifs

It can find the optimal width and number of given motifs in each sequence

Which of the following is untrue about CLUSTAL program?

The initial step includes performing pair-wise alignments of all of the sequences

CLUSTAL performs a global-multiple sequence alignment by a different method than MSA (Multiple Sequence Alignment)

The initial heuristic alignment obtained by MSA is calculated in a different way

The initial step includes performing pair-wise alignments of all of the sequences

The intermediate step includes use the alignment scores to produce a phylogenetic tree

Which of the following is not among the methods for finding localized sequence similarity?

Extraction of Blocks from a Global or Local MSA

The number of possible global alignments between two sequences of length N is _____

\(\frac{2^{(N-1)}}{\sqrt{πN}}\)

Which of the following is untrue about Protein substitution matrices?

They are significantly more complex than DNA scoring matrices

They have the N x N matrices of the amino acids

Protein substitution matrices have quite important role in evolutionary studies

They are significantly quite less complex than DNA scoring matrices

Which of the following is incorrect regarding PRRP?

The whole process is repeated until there is no further increase in the alignment score

The program PRRP uses iterative methods to produce an alignment

An initial pair-wise alignment is made to predict a tree

The whole process is repeated until there is no further increase in the alignment score

Which of the following is untrue about iterative approach?

The iterative approach is based on the idea that an optimal solution can be found by repeatedly modifying existing suboptimal solutions

Because the order of the sequences used for alignment is different in each iteration

This method is also heuristic in nature and does not have guarantees for finding the optimal alignment

This method is not based on heuristic methods

Which of the following is not true regarding the BLOCKS?

The BLOCKS server can extract a conserved, ungapped region from a MSA to produce a sequence block

The server can also find blocks in a set of unaligned, input sequences and maintains a large database of blocks based on an analysis of proteins in the Prosite catalog

Blocks are found by the Protomat program

The program MOTIF doesn’t locate spaced patterns

Which of the following is untrue about DCA?

It stands for Divide-and-Conquer Alignment

It works by breaking each of the sequences into two smaller sections

The breaking points during the process are determined based on regional similarity of the sequences

If the sections are not short enough, further divisions are restricted as well

Which of the following is untrue regarding T-Coffee?

The local pair wise alignment is generated by the Lalign program, from which the top ten scored alignments are selected

It stands for Tree-based Consistency Objective Function for alignment Evaluation

It performs progressive sequence alignments as in Clustal.

The global pair wise alignment is not performed using the Clustal program.

The local pair wise alignment is generated by the Lalign program, from which the top ten scored alignments are selected

The initial alignments used to produce the guide tree may be obtained by various methods. Which of the following is not one of them?

pattern-finding approach similar

Faster, full dynamic programming method

Which of the following is untrue about PRRN?

PRRN is a web-based program that uses a double nested iterative strategy for multiple alignment

It performs multiple alignments through two sets of iterations: inner iteration and outer iteration

In the outer iteration, an initial random alignment is generated that is used to derive a UPGMA tree

In the inner iteration, the sequences are randomly divided into multiple groups

Which of the following about MEME is untrue?

It is a Web resource for performing local MSAs (Multiple Sequence Alignment) by the above expectation maximization method is the program MEME

It stands for Multiple EM for Motif Elicitation

It was developed at developed at the University of California at San Diego Supercomputing Center

The Web page has multiple versions for searching blocks by an EM algorithm

Which of the following is untrue about PILEUP program?

The sequences are aligned pair-wise using the Needleman- Wunsch dynamic programming algorithm

It is the MSA program that is a part of the Genetics Computer Group package of sequence analysis programs

It is owned since 1997 by Oxford Communications and is widely used due to the popularity and availability of this package

It uses a method for MSA that is polar opposite to CLUSTALW

The sequences are aligned pair-wise using the Needleman- Wunsch dynamic programming algorithm

Which of the following is untrue about Needleman-Wunsch algorithm?

It was first used by Saul Needleman and Christian Wunsch

It is an example of dynamic programming

Basic idea here is to build up the best alignment by using optimal alignments of larger subsequences

It was first used by Saul Needleman and Christian Wunsch

If a good sampling of sequences is _______ the number of sequences is _________ and the motif structure is ________ it should, in principle, be possible to obtain frequencies highly representative of the same motif in other sequences also.

unavailable, sufficiently large, not too complex

available, sufficiently large, not too complex

unavailable, sufficiently large, not too complex

unavailable, sufficiently small, not too complex

available, sufficiently large, too complex

Which of the following is untrue about DIALIGN2?

It does not apply gap penalties and thus is not sensitive to long gaps

It is a web based program designed to detect local similarities

It is designed to detect global similarities

It does not apply gap penalties and thus is not sensitive to long gaps

The method breaks each of the sequences down to smaller segments and performs all possible pair wise alignments between the segments

Which of the following is untrue regarding the block analysis method?

Blocks represent a conserved region in the MSA

Blocks differ from profiles in lacking insert and delete positions in the sequences

Every column includes only matches and mismatches

Blocks may be made by searching for a section of an MSA alignment that is low conserved

78 + Mcqs in Multiple Sequence Alignment in Bioinformatics Page 1 McqOptions

1.	Which of the following is untrue regarding Expectation Maximization algorithm?
A.	An initial guess is made as to the location and size of the site of interest in each of the sequences, and these parts of the sequence are aligned
B.	The alignment provides an estimate of the base or amino acid composition of each column in the site
C.	The column-by-column composition of the site already available is used to estimate the probability of finding the site at any position in each of the sequences
D.	The row-by-column composition of the site already available is used to estimate the probability
Answer» E.

2.	In the initial step of EM algorithm, the 20-residue-long binding motif patterns in each sequence are aligned as an initial guess of the motif.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

3.	The program Profilemake can be used to produce a profile from an MSA.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

4.	Out of the two repeated steps in EM algorithm, the step 2 is ________
A.	the maximization step
B.	the minimization step
C.	the optimization step
D.	the normalization step
Answer» B. the minimization step

5.	The pattern searching method type of analysis was performed on groups of related proteins, and the amino acid patterns that were located may be found in the Prosite catalog.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

7.	Analysis of MSAs for conserved blocks of sequence leads to production of the position-specific scoring matrix.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

9.	Which of the following is not among the methods for finding localized sequence similarity?
A.	Profile Analysis
B.	Block Analysis
C.	Extraction of Blocks from a Global or Local MSA
D.	Pattern blocking
Answer» E.

10.	The number of possible global alignments between two sequences of length N is _____
A.	\(\frac{2^N}{\sqrt{πN}}\)
B.	\(\frac{2^{2N}}{\sqrt{πN}}\)
C.	\(\frac{2^{(N-1)}}{\sqrt{πN}}\)
D.	\(\frac{2^{2N}}{\sqrt{N}}\)
Answer» C. \(\frac{2^{(N-1)}}{\sqrt{πN}}\)

11.	Match-Box compares segments of some of the nine residues of possible Pair wise alignments.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

14.	Iterative methods include repeatedly realigning subgroups of the sequences and then by aligning these subgroups into a local alignment of all of the sequences.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

15.	The scoring of gaps in a MSA (Multiple Sequence Alignment) has to be performed in a different manner from scoring gaps in a pair-wise alignment.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

20.	CLUSTALW is a more recent version of CLUSTAL with the W standing for ________
A.	weakening
B.	winding
C.	weighting
D.	wiping
Answer» D. wiping

16.	In Needleman-Wunsch algorithm, the gaps are scored -2.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

17.	An alternative method is to produce an odds scoring matrix calculated by dividing each base frequency by the background frequency of that base.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

18.	Although MOTIF program is used successfully for making the BLOCKS database, it is limited in the pattern sizes that can be found.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

19.	Block analysis methods use substitution matrices such as the PAM and BLOSUM matrices to score matches.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

21.	An approach for obtaining a higher-scoring MSA (Multiple Sequence Alignment) by rearranging an existing alignment uses a probability approach called simulated annealing.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

22.	The CLUSTALX provides a graphic interface.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

23.	Given a multiple alignment of three sequences, the sum of scores is calculated as the sum of the dissimilarity scores of every pair of sequences at each position.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

24.	There are two approaches viz. exhaustive and heuristic approaches used in multiple sequence alignment.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

25.	As the amount of computational time and memory space required increases exponentially with the number of sequences, it makes the multidimensional search matrix method computationally prohibitive to use for a large data set.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

28.	The Expectation Maximization algorithm has been used to identify conserved domains in unaligned proteins only.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Explore topic-wise MCQs in Bioinformatics.

Which of the following is untrue regarding Expectation Maximization algorithm?

In the initial step of EM algorithm, the 20-residue-long binding motif patterns in each sequence are aligned as an initial guess of the motif.

The program Profilemake can be used to produce a profile from an MSA.

Out of the two repeated steps in EM algorithm, the step 2 is ________

The pattern searching method type of analysis was performed on groups of related proteins, and the amino acid patterns that were located may be found in the Prosite catalog.

Which of the following about the Gibbs sampler is untrue?

Analysis of MSAs for conserved blocks of sequence leads to production of the position-specific scoring matrix.

Which of the following is untrue about CLUSTAL program?

Which of the following is not among the methods for finding localized sequence similarity?

The number of possible global alignments between two sequences of length N is _____

Match-Box compares segments of some of the nine residues of possible Pair wise alignments.

Which of the following is untrue about Protein substitution matrices?

Which of the following is incorrect regarding PRRP?

Iterative methods include repeatedly realigning subgroups of the sequences and then by aligning these subgroups into a local alignment of all of the sequences.

The scoring of gaps in a MSA (Multiple Sequence Alignment) has to be performed in a different manner from scoring gaps in a pair-wise alignment.

In Needleman-Wunsch algorithm, the gaps are scored -2.

An alternative method is to produce an odds scoring matrix calculated by dividing each base frequency by the background frequency of that base.

Although MOTIF program is used successfully for making the BLOCKS database, it is limited in the pattern sizes that can be found.

Block analysis methods use substitution matrices such as the PAM and BLOSUM matrices to score matches.

CLUSTALW is a more recent version of CLUSTAL with the W standing for ________

An approach for obtaining a higher-scoring MSA (Multiple Sequence Alignment) by rearranging an existing alignment uses a probability approach called simulated annealing.

The CLUSTALX provides a graphic interface.

Given a multiple alignment of three sequences, the sum of scores is calculated as the sum of the dissimilarity scores of every pair of sequences at each position.

There are two approaches viz. exhaustive and heuristic approaches used in multiple sequence alignment.

As the amount of computational time and memory space required increases exponentially with the number of sequences, it makes the multidimensional search matrix method computationally prohibitive to use for a large data set.

Which of the following is untrue about iterative approach?

Which of the following is not true regarding the BLOCKS?

The Expectation Maximization algorithm has been used to identify conserved domains in unaligned proteins only.

There are two types matrices involved in the study- score matrices and trace matrices.

Profiles are found by performing the _____ MSA of a group of sequences and then removing the _______ regions in the alignment into a smaller MSA.

Clustal is a progressive multiple alignment program available either as a stand-alone or on-line program.

Which of the following is untrue about DCA?

Which of the following is untrue regarding T-Coffee?

The initial alignments used to produce the guide tree may be obtained by various methods. Which of the following is not one of them?

The alignment score is the sum of substitution scores and gap penalties in this type of algorithm.

Which of the following is untrue about PRRN?

Which of the following about MEME is untrue?

The major drawback of the progressive and iterative alignment strategies is that they are largely global alignment based and may therefore fail to recognize conserved domains and motifs among highly divergent sequences of varying lengths.

Which of the following is untrue about PILEUP program?

Which of the following is untrue about Needleman-Wunsch algorithm?

If a good sampling of sequences is _______ the number of sequences is _________ and the motif structure is ________ it should, in principle, be possible to obtain frequencies highly representative of the same motif in other sequences also.

Which of the following is untrue about DIALIGN2?

Which of the following is untrue regarding the block analysis method?

The global sequence alignment is suitable when the two sequences are of dissimilar length, with a negligible degree of similarity throughout.

Progenitor sequences represented by the ______ branches of the tree are derived by alignment of the _______ sequences.

The substitution matrices are rarely used in this type of matching.

GDE (Genetic Data Environment) provides a general interface on UNIX machines for sequence analysis, sequence alignment editing, and display.

Two commonly encountered examples are the Genetics Computer Group’s MSF format and the CLUSTALW ALN format.

The HMM is a statistical model that considers few combinations of matches and gaps to generate an alignment of a set of sequences.

Profiles are found by performing the _ MSA of a group of sequences and then removing the ___ regions in the alignment into a smaller MSA.

If a good sampling of sequences is ___ the number of sequences is _ and the motif structure is ____ it should, in principle, be possible to obtain frequencies highly representative of the same motif in other sequences also.

Progenitor sequences represented by the branches of the tree are derived by alignment of the _ sequences.

30.	Profiles are found by performing the _____ MSA of a group of sequences and then removing the _______ regions in the alignment into a smaller MSA.
A.	local, more highly conserved
B.	global, low conserved
C.	global, more highly conserved
D.	local, low conserved
Answer» D. local, low conserved

34.	The initial alignments used to produce the guide tree may be obtained by various methods. Which of the following is not one of them?
A.	Fast k-tuple
B.	pattern-finding approach similar
C.	FASTA
D.	Faster, full dynamic programming method
Answer» E.

41.	In EM algorithm, as an example, suppose that there are 10 DNA sequences having very little similarity with each other, each about 100 nucleotides long and thought to contain a binding site near the middle 20 residues, based on biochemical and genetic evidence. The following steps would be used by the EM algorithm to find the most probable location of the binding sites in each of the ______ sequences.
A.	30
B.	10
C.	25
D.	20
Answer» C. 25

46.	Progenitor sequences represented by the ______ branches of the tree are derived by alignment of the _______ sequences.
A.	outer, outermost
B.	inner, outermost
C.	inner, innermost
D.	outer, innermost
Answer» C. inner, innermost