Questions and answers for exam Preparation

MCQs

Total Questions : 150 | Page 1 of 15 pages

Question 1. Which of the following does not describe PAM matrices?

These matrices are used in optimal alignment scoring
It stands for Point Altered Mutations
It stands for Point Accepted Mutations
It was first developed by Margaret Dayhoff

Discuss Question

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?

Score can be negative in this method
It is based on dynamic programming technique
For two sequences of length m and n, the matrix to be defined should be of dimensions m+1 and n+1
For two sequences of length m and n, the matrix to be defined should be of dimensions m and n

Discuss Question

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?

It attempts to align every residue in every sequence
It is most useful when the aligning sequences are similar and of roughly the same size
It is useful when the aligning sequences are dissimilar
It can use Needleman-Wunsch algorithm

Discuss Question

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?

They determine likelihood of homology between two sequences
They use system where substitutions that are more likely should get a higher score
They use system where substitutions that are less likely should get a lower score
BLOSUM-X type uses logarithmic identity to find similarity

Discuss Question

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?

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
If the residues are not same, the mismatch score is assumed as -3
If the residues are not same, the mismatch score is assumed as 3
The score should be added to the diagonally positioned cell of the current cell

Discuss Question

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?

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

Discuss Question

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?

Closely related sequences
Distinctly related sequences
Distinctly related sequences that share common motifs
Closely related sequences that share common motifs

Discuss Question

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?

The log odds scores of the PSSM are modified at the end of the process
The procedure stops prematurely if the scores reach convergence
The final result is not sensitive to the initial alignment
Local optimum is an advantage of EM method

Discuss Question

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.