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Multiple Sequence Alignment Online Exam Quiz

Important questions about Multiple Sequence Alignment. Multiple Sequence Alignment MCQ questions with answers. Multiple Sequence Alignment exam questions and answers for students and interviews.

Related sequences are identified through the database similarity searching and as the process generates multiple matching sequence pairs, it is often necessary to convert the numerous pair wise alignments into a single alignment.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

There is a unique advantage of multiple sequence alignment because it reveals more biological information than many pair wise alignments can.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following cannot be related to multiple sequence alignment?

Options

A : a. Many conserved and functionally critical amino acid residues can be identified in a protein multiple alignment

B : b. Multiple sequence alignment is also an essential prerequisite to carrying out phylogenetic analysis of sequence families and prediction of protein secondary and tertiary structures

C : c. Multiple sequence alignment also has applications in designing degenerate polymerase chain reaction (PCR) primers based on multiple related sequences

D : d. This method does not contribute much to degenerate polymerase chain reaction (PCR) primers creation

The scoring function for multiple sequence alignment is based on the concept of sum of pairs (SP).

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following scores are not considered while calculating the SP scores?

Options

A : a. All possible pair wise matches

B : b. All possible mismatches

C : c. All possible gap costs

D : d. Number of gap penalties

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.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

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

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

In a multidimensional search matrix, for aligning N sequences, an (N+2)-dimensional matrix is needed to be filled with alignment scores.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

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.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following is untrue about DCA?

Options

A : a. It stands for Divide-and-Conquer Alignment

B : b. It works by breaking each of the sequences into two smaller sections

C : c. The breaking points during the process are determined based on regional similarity of the sequences

D : d. If the sections are not short enough, further divisions are restricted as well

Which of the following is untrue regarding the Progressive Alignment Method?

Options

A : a. Progressive alignment depends on the stepwise assembly of multiple alignments and is heuristic in nature

B : b. It speeds up the alignment of multiple sequences through a multistep process

C : c. It first conducts pair wise alignments for each possible pair of sequences using the Needleman–Wunsch global alignment method and records these similarity scores from the pair wise comparisons

D : d. Its drawback is it slows down the alignment of multiple sequences through a single step process

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

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following is not a drawback of the progressive alignment method?

Options

A : a. The progressive alignment method is not suitable for comparing sequences of different lengths because it is a global alignment–based method

B : b. In this method the use of affine gap penalties, long gaps are not allowed, and, in some cases, this may limit the accuracy of the method

C : c. In this method the use of affine gap penalties, long gaps is allowed, and, in some cases, this may limit the accuracy of the method

D : d. The final alignment result is also influenced by the order of sequence addition

Which of the following is untrue regarding T-Coffee?

Options

A : a. It stands for Tree-based Consistency Objective Function for alignment Evaluation

B : b. It performs progressive sequence alignments as in Clustal.

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

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

Which of the following is untrue about iterative approach?

Options

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

B : b. Because the order of the sequences used for alignment is different in each iteration

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

D : d. This method is not based on heuristic methods

Which of the following is untrue about PRRN?

Options

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

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

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

D : d. In the inner iteration, the sequences are randomly divided into multiple groups

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.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following is untrue about DIALIGN2?

Options

A : a. It is a web based program designed to detect local similarities

B : b. It is designed to detect global similarities

C : c. It does not apply gap penalties and thus is not sensitive to long gaps

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

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

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following is not the objective to perform sequence comparison?

Options

A : a. To observe patterns of conservation

B : b. To find the common motifs present in both sequences

C : c. To study the physical properties of molecules

D : d. To study evolutionary relationships

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