Sequence Alignment(Bioinformatics ) Questions and Answers

Question 1. Which of the following does not describe PAM matrices?
  1.    These matrices are used in optimal alignment scoring
  2.    It stands for Point Altered Mutations
  3.    It stands for Point Accepted Mutations
  4.    It was first developed by Margaret Dayhoff
Explanation:-
Answer: Option B. -> It stands for Point Altered Mutations
Answer: (b).It stands for Point Altered Mutations
Question 2. Which of the following does not describe global alignment algorithm?
  1.    Score can be negative in this method
  2.    It is based on dynamic programming technique
  3.    For two sequences of length m and n, the matrix to be defined should be of dimensions m+1 and n+1
  4.    For two sequences of length m and n, the matrix to be defined should be of dimensions m and n
Explanation:-
Answer: Option D. -> For two sequences of length m and n, the matrix to be defined should be of dimensions m and n
Answer: (d).For two sequences of length m and n, the matrix to be defined should be of dimensions m and n
Question 3. Which of the following does not describe global alignment algorithm?
  1.    It attempts to align every residue in every sequence
  2.    It is most useful when the aligning sequences are similar and of roughly the same size
  3.    It is useful when the aligning sequences are dissimilar
  4.    It can use Needleman-Wunsch algorithm
Explanation:-
Answer: Option C. -> It is useful when the aligning sequences are dissimilar
Answer: (c).It is useful when the aligning sequences are dissimilar
Question 4. Which of the following is wrong in case of substitution matrices?
  1.    They determine likelihood of homology between two sequences
  2.    They use system where substitutions that are more likely should get a higher score
  3.    They use system where substitutions that are less likely should get a lower score
  4.    BLOSUM-X type uses logarithmic identity to find similarity
Explanation:-
Answer: Option D. -> BLOSUM-X type uses logarithmic identity to find similarity
Answer: (d).BLOSUM-X type uses logarithmic identity to find similarity
Question 5. Which of the following is untrue regarding the scoring system used in dynamic programming?
  1.    If the residues are same in both the sequences the match score is assumed as +5 which is added to the diagonally positioned cell of the current cell
  2.    If the residues are not same, the mismatch score is assumed as -3
  3.    If the residues are not same, the mismatch score is assumed as 3
  4.    The score should be added to the diagonally positioned cell of the current cell
Explanation:-
Answer: Option C. -> If the residues are not same, the mismatch score is assumed as 3
Answer: (c).If the residues are not same, the mismatch score is assumed as 3
Question 6. Which of the following is untrue about Expectation Maximization (EM) method?
  1.    It is used to find hidden motifs
  2.    The method works by first making a random or guessed alignment of the sequences to generate a trial PSSM
  3.    The trial PSSM is used to compare with each sequence individually
  4.    The log odds scores of the PSSM are modified at the end of the process
Explanation:-
Answer: Option D. -> The log odds scores of the PSSM are modified at the end of the process
Answer: (d).The log odds scores of the PSSM are modified at the end of the process
Question 7. For what type of sequences Gibbs sampling is used?
  1.    Closely related sequences
  2.    Distinctly related sequences
  3.    Distinctly related sequences that share common motifs
  4.    Closely related sequences that share common motifs
Explanation:-
Answer: Option C. -> Distinctly related sequences that share common motifs
Answer: (c).Distinctly related sequences that share common motifs
Question 8. Which of the following is true about Expectation Maximization (EM) method?
  1.    The log odds scores of the PSSM are modified at the end of the process
  2.    The procedure stops prematurely if the scores reach convergence
  3.    The final result is not sensitive to the initial alignment
  4.    Local optimum is an advantage of EM method
Explanation:-
Answer: Option B. -> The procedure stops prematurely if the scores reach convergence
Answer: (b).The procedure stops prematurely if the scores reach convergence
Question 9. In the web-based program MEME, the computation is a _____ step procedure.
  1.    one
  2.    two
  3.    three
  4.    four
Explanation:-
Answer: Option B. -> two
Answer: (b).two
Question 10. MEME stands for _____________
  1.    Multiple Expectation Maximization for Motif Elicitation
  2.    Multiple Expectation Maximization for Motif Extraction
  3.    Mega Expectation Maximization for Motif Elicitation
  4.    Micro Expectation Maximization for Motif Extraction
Explanation:-
Answer: Option A. -> Multiple Expectation Maximization for Motif Elicitation
Answer: (a).Multiple Expectation Maximization for Motif Elicitation
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