Category: Objective Questions

Bioinformatics Multiple Choice Questions on “Exhaustive Algorithms”.

1. 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.
A. True
B. False

Answer: A
Explanation: A natural extension of pair wise alignment is multiple sequence alignment, which is to align multiple related sequences to achieve optimal matching of the sequences. Related sequences are identified through the database similarity searching. As the process generates multiple matching sequence pairs, it is often necessary to convert the numerous pair wise alignments into a single alignment, which arranges sequences in such a way that evolutionarily equivalent positions across all sequences are matched.

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

Answer: A
Explanation: It is truly an advantage of multiple sequence alignment. For example, it allows the identification of conserved sequence patterns and motifs in the whole sequence family, which are not obvious to detect by comparing only two sequences.

3. Which of the following cannot be related to multiple sequence alignment?
A. Many conserved and functionally critical amino acid residues can be identified in a protein multiple alignment
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. Multiple sequence alignment also has applications in designing degenerate polymerase chain reaction (PCR) primers based on multiple related sequences
D. This method does not contribute much to degenerate polymerase chain reaction (PCR) primers creation

Answer: D
Explanation: In practice, heuristic approaches are most often used. Multiple sequence alignment has applications in designing degenerate (PCR) primers based on multiple related sequences.

4. The scoring function for multiple sequence alignment is based on the concept of sum of pairs (SP).
A. True
B. False

Answer: A
Explanation: Multiple sequence alignment is to arrange sequences in such a way that a maximum number of residues from each sequence are matched up according to a particular scoring function and is based on the concept of sum of pairs (SP). As the name suggests, it is the sum of the scores of all possible pairs of sequences in a multiple alignment based on a particular scoring matrix.

5. Which of the following scores are not considered while calculating the SP scores?
A. All possible pair wise matches
B. All possible mismatches
C. All possible gap costs
D. Number of gap penalties

Answer: D
Explanation: In calculating the SP scores, each column is scored by summing the scores for all possible pair wise matches, mismatches and gap costs. The score of the entire alignment is the sum of all of the column scores. The score of the entire alignment is the sum of all of the column scores. In that case, option d becomes irrelevant choice here.

6. 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

Answer: B
Explanation: Given a multiple alignment of three sequences, the sum of scores is calculated as the sum of the similarity scores of every pair of sequences at each position. The scoring is based on the BLOSUM62 matrix. If the total score for the alignment is 5, which means that the alignment is 25 = 32 times more likely to occur among homologous sequences than by random chance.

7. There are two approaches viz. exhaustive and heuristic approaches used in multiple sequence alignment.
A. True
B. False

Answer: A
Explanation: The exhaustive alignment method involves examining all possible aligned positions simultaneously. Similar to dynamic programming in pair wise alignment, which involves the use of a two-dimensional matrix to search for an optimal alignment, to use dynamic programming for multiple sequence alignment, extra dimensions are needed to take all possible ways of sequence matching into consideration.

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

Answer: B
Explanation: In a multidimensional search matrix, for aligning N sequences, an N-dimensional matrix is needed to be filled with alignment scores. For instance, for three sequences, a three-dimensional matrix is required to account for all possible alignment scores. Back-tracking is applied through the three-dimensional matrix to find the highest scored path that represents the optimal alignment.

9. 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

Answer: A
Explanation: This is indeed the drawback of that method. For this reason, full dynamic programming is limited to small datasets of less than ten short sequences. For the same reason, few multiple alignment programs employing this “brute force” approach are publicly available.

10. Which of the following is untrue about DCA?
A. It stands for Divide-and-Conquer Alignment
B. It works by breaking each of the sequences into two smaller sections
C. The breaking points during the process are determined based on regional similarity of the sequences
D. If the sections are not short enough, further divisions are restricted as well

Answer: D
Explanation: This is a web-based program that is in fact semi exhaustive because certain steps of computation are reduced to heuristics. If the sections are not short enough, further divisions are carried out. When the lengths of the sequences reach a predefined threshold, dynamic programming is applied for aligning each set of subsequences. The resulting short alignments are joined together head to tail to yield a multiple alignment of the entire length of all sequences.

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Bioinformatics Multiple Choice Questions on “Ab Initio Approach”.

1. In dot matrix in ab initio methods, the diagonals _____________ to the main diagonal represent regions that can self hybridize.
A. parallel
B. cutting in random fashion
C. perpendicular
D. adjacent parallel

Answer: c
Explanation: The diagonals perpendicular to the main diagonal represent regions that can self hybridize to form double-stranded structure with traditional A–U and G–C base pairs. In reality, the pattern detection in a dot matrix is often obscured by high noise levels.

2. 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

Answer: B
Explanation: To reduce the noise in the matrix is to select an appropriate window size of a minimum number of contiguous base matches. Normally, only a window size of four consecutive base matches is used. If the dot plot reveals more than one feasible structure, the lowest energy one is chosen.

3. 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: c
Explanation: Mostly, The use of a dot plot can be effective in finding a single secondary structure in a small Molecule. However, if a large molecule contains multiple secondary structure segments, choosing a combination that is energetically most stable among a large number of possibilities can be a daunting task.

4. In ab initio methods, a quantitative approach such as dynamic programming can be used to assemble a final structure with optimal base-paired regions.
A. True
B. False

Answer: A
Explanation: In this approach, an RNA sequence is compared with itself. A scoring scheme is applied to fill the matrix with match scores based on Watson–Crick base complementarity.

5. In dynamic programming, in ab initio methods, Often ________ base pairing and energy terms of the base pairing _____ incorporated into the scoring process.
A. G-C, are
B. G–U, are not
C. G–U, are also
D. G-C, are not

Answer: c
Explanation: Although the traditional structure comprises of A–U and G–C base pairs, G-U base pairing is incorporated into the scoring process. A path with the maximal score within a scoring matrix after taking into account the entire sequence information represents the most probable secondary structure form.

6. The dynamic programming method produces ____ structure with _____ score.
A. one, single best
B. multiple, single best
C. multiple, multiple
D. single, multiple

Answer: A
Explanation: However, this is potentially a drawback of this approach. In reality an RNA may exist in multiple alternative forms with near minimum energy but not necessarily the one with maximum base pairs.

7. The problem of dynamic programming to select one single structure can be complemented by adding a probability distribution function, known as the _________ which calculates a mathematical distribution of probable base pairs in thermodynamic equilibrium.
A. partition function
B. division function
C. increment function
D. fold function

Answer: A
Explanation: This function helps to select a number of suboptimal structures within a certain energy range. The MFOLD and RNAFold are two well-known programs using the ab initio prediction method.

8. Which of the following is correct about MFOLD?
A. It uses the dynamic programming only
B. It uses the thermodynamic calculations only
C. It uses the both dynamic programming and thermodynamic calculations as well
D. It doesn’t take into account the themoststablility of the secondary structures

Answer: B
Explanation: It is a web-based program for RNA secondary structure prediction. It combines dynamic programming and thermodynamic calculations for identifying themostable secondary structures with the lowest energy. It also produces dot plots coupled with energy terms. This method is reliable for short sequences but becomes less accurate as the sequence length increases.

9. Like Mfold, RNAfold only examines the energy terms of the optimal alignment in a dot plot.
A. True
B. False

Answer: B
Explanation: It is one of the web programs in the Vienna package. Unlike Mfold, which only examines the energy terms of the optimal alignment in a dot plot, RNAfold extends the sequence alignment to the vicinity of the optimal diagonals to calculate thermodynamic stability of alternative structures.

10. Which of the following about the RNAFold is incorrect?
A. It extends the sequence alignment to the vicinity of the optimal diagonals to calculate thermodynamic stability of alternative structures
B. It incorporates a partition function
C. It doesn’t necessarily use a partition function
D. It aims to select a number of statistically most probable structures in one of its steps

Answer: c
Explanation: Based on both thermodynamic calculations and the partition function, a number of alternative structures that may be suboptimal are provided. The collection of the predicted structures may provide a better estimate of plausible foldings of an RNA molecule than the predictions by Mfold.

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Genetic Engineering Multiple Choice Questions on “Categories of Ligation Reaction”.

1. Ligation is defined as ______________
a) Alignment of only double stranded DNA molecules at the ends and the formation of phosphodiester bonds between both the strands
b) Alignment of either of the double or single stranded DNA molecules and formation of glycosidic bonds between both the strands
c) Alignment of either of the double or single stranded DNA molecules and the formation of phosphodiester bonds. The bond can be between either one or both the strands
d) Alignment of single stranded DNA molecules and formation of glycosidic bonds between these strands
Answer: c
Explanation: Ligation is basically the formation of bonds between the ends of two DNA strands. The strands can be single or double. The nature of the bond is phosphodiester, which means that bond is formed between sugar and phosphate. The phosphodiester bond can either be formed between one strand or both the strands.

2. If only one bond is broken in the sugar-phosphate backbone, it is called as ___________
a) gap
b) nick
c) break
d) leakage
Answer: b
Explanation: In the case, if only one bond is broken in the sugar phosphate backbone, it is termed as nick. If a number of nucleotides are missing, it is termed a gap. Nick can be sealed by ligation reactions but gap can’t be sealed by a ligation reaction.

3. How many categories of ligation reaction are there on the basis of ends created?
a) 1
b) 2
c) 3
d) 4
Answer: b
Explanation: There are two categories of ligation reaction and are named as blunt-ended and sticky ended reaction. They are named because of the nature of the ends of the molecules to be ligated.

4. In the case of blunt-end ligation, blunt ends can be generated by ___________
a) simply the action of restriction endonuclease which gives straight ends
b) the polishing of staggered ends
c) both the action of restriction endonuclease which gives straight ends and polishing of staggered ends
d) by the action of restriction endonuclease which gives staggered ends
Answer: c
Explanation: Blunt ends are those which don’t have single stranded ends as overhangs. The ends are double stranded. And these can be generated by polishing the staggered ends or the action of restriction endonuclease which generate straight ends.

5. The ligation reaction is more efficient in which case?
a) Blunt end ligation
b) Sticky end ligation
c) Both have the same efficiency
d) Depends on the reaction conditions
Answer: b
Explanation: Sticky end ligation is generally more efficient than blunt end ligation. It is so because sticky end ligation is carried out because of complementary base pairing.

6. The sticky ends are held together by which type of bonds?
a) Hydrogen bond
b) Covalent bond
c) Ionic bond
d) Van-der-waal forces
Answer: a
Explanation: The sticky ends are held together by the hydrogen bonds. Hydrogen bonds are weak in nature and can easily be broken.

7. Why sticky ended ligations are carried out at temperatures lower than room temperature?
a) It is so because the vibrational and kinetic energy of the molecules at room temperature is lower than that of the energy required to break the bonds holding the ends
b) The energy required to break the bonds holding the ends is very less than that of the kinetic and vibrational energy at room temperature
c) The enzyme carrying out ligation is unstable at low temperature
d) The sticky ends created, don’t just relegate at low temperature
Answer: a
Explanation: The sticky ends are held together by the hydrogen bonds. These hydrogen bonds are weak in nature and the energy required to break them is very less than the kinetic and vibrational energy of the molecules at room temperature. Hence the reaction is carried at 4 degrees.

8. Ligation reaction can be both intramolecular and intermolecular in nature.
a) True
b) False
Answer: a
Explanation: Ligation reaction can be both intramolecular and intermolecular in nature. The intermolecular reaction is that which ends ligated are of two different molecules. The intramolecular ligation is that which ends ligated belong to the same molecule.

9. If a ligation reaction is being carried out and recircularization is observed, which type of reaction is being carried out?
a) Intramolecular
b) Intermolecular
c) Both observe recircularization equally
d) Recirculation is not possible in any of the cases
Answer: a
Explanation: Recircularization is the phenomenon of joining the ends of the same molecule. It happens in the case of intramolecular ligation reaction.

10. What is the kinetics of the intramolecular and intermolecular ligation reactions?
a) Second order kinetics for intramolecular and first order for intermolecular
b) First order kinetics for intramolecular and second order for intermolecular
c) Both are first order
d) Both are second order
Answer: b
Explanation: As the intramolecular reaction requires only the type of reaction species, the reaction is first order.Whereas, on the other hand intermolecular reaction requires collision between two different species and hence it is second order reaction.

11. What are the effects of increasing concentration of reaction components?
a) It increases chances of ligation in both intramolecular and intermolecular reactions
b) It increases chances of ligation only in intermolecular and no effect on intramolecular
c) It decreases chances of ligation in intramolecular and increases in that of intermolecular
d) It decreases chances of ligation in both types of reaction
Answer: b
Explanation: As the concentration of reaction components is increased, there are increased chances of ligation in intermolecular reaction because of frequency of collision of two different molecules increases. The intramolecular reaction is unaffected because the probability of meeting the ends of a molecule remains the same.