Question 2 MCQ · 2.0 marks
A published solution is not available for this question yet.
Algorithmic Thinking in Bioinformatics · Quiz 2 · Jan 2025
Algorithmic Thinking in Bioinformatics · Quiz 2 · Jan 2025
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Question 3 MCQ · 3.0 marks
A published solution is not available for this question yet.
Question 4 MCQ · 5.0 marks
Figure I: Gibbs Sampling; Figure II: Randomized Motif Search; Figure III:
Greedy Motif Search
Figure I: Gibbs Sampling; Figure II: Greedy Motif Search; Figure III:
Randomized Motif Search
Figure I: Greedy Motif Search; Figure II: Randomized Motif Search; Figure III:
Gibbs Sampling
Figure I: Randomized Motif Search; Figure II: Gibbs Sampling; Figure III:
Greedy Motif Search
A published solution is not available for this question yet.
Question 5 NAT · 2.0 marks
The number of leaves in the suffix tree (including the $ symbol) of a genome sequence is 15 and
the number of elements in the Burrows-Wheeler matrix is 225. What is the length of the original
genome sequence (including the $ symbol)?
Enter the value as a single integer.
A published solution is not available for this question yet.
Question 6 NAT · 2.0 marks
What is the maximum possible length of the run-length encoding of a genome sequence of length
50. (Hint: Beware that the length of a run-length encoding of a string should include both the
counts and the characters in the encoded string.)
A published solution is not available for this question yet.
Question 7 MSQ · 2.0 marks
Recall that if the distance matrix is additive, then there is a unique simple tree that fits this matrix.
Suppose you are given an additive distance matrix D and you construct two phylogenies from D.
The first phylogeny T1 is constructed using the Additive Phylogeny algorithm, while the second
phylogeny T2 is constructed using the Neighbor Joining algorithm. Choose all the statements
which are correct about the two trees.
T1 and T2 have the same leaves.
T1 and T2 have the same cherries.
T1 and T2 are identical
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Question 8 MSQ · 4.0 marks
Based on the above data, answer the given subquestions.
A published solution is not available for this question yet.
Question 9 NAT · 3.0 marks
Based on the above data, answer the given subquestions.
A published solution is not available for this question yet.
Question 10 MSQ · 4.0 marks
Based on the above data, answer the given subquestions.
A published solution is not available for this question yet.
Question 11 MCQ · 3.0 marks
Based on the above data, answer the given subquestions.
What is the probability of observing data point 7 according to this model?
A published solution is not available for this question yet.
Question 12 NAT · 3.0 marks
Based on the above data, answer the given subquestions.
Given that data point 7 is observed, what is the probability that the observation is from
component A?
Round your answer to 3 decimal digits.
A published solution is not available for this question yet.
Question 13 MSQ · 3.0 marks
Based on the above data, answer the given subquestions.
We say a person S does not have the disease X (i.e., S is healthy) if the sample read collected (from
S) does not have any mutation. The options given below are the reads collected from different
individuals. Match the reads with the suffix tree to identify which among these individuals suffer
from the disease? Choose all the options that apply.
TCAAC
ATGCC
AGCCG
ACGGT
CCGGG
A published solution is not available for this question yet.
Question 14 MCQ · 3.0 marks
Based on the above data, answer the given subquestions.
Use the given suffix tree to determine which of the following is the suffix array for the reference
human genome without finding the reference genome? Assume $ comes first in the alphabet.
[13, 5, 6, 0, 4, 7, 8, 9, 10, 11, 2, 12, 3, 1]
[13, 12, 3, 1, 2, 11, 10, 9, 8, 7, 4, 6, 5, 0]
[0, 5, 6, 4, 7, 8, 9, 10, 11, 2, 1, 3, 12, 13]
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13]
A published solution is not available for this question yet.
Question 15 MCQ · 3.0 marks
Based on the above data, answer the given subquestions.
You are trying to read the entire genome sequence of a new individual. But due to a technical
problem, the machine could read the first 7 nucleotides only. Later you learn that the individual is
not affected by the disease X. Which of the following reads is the string that the machine could not
read?
CCGGG$
TCAAC$
AGCCG$
ATGCC$
CGGGT$
A published solution is not available for this question yet.
Question 16 MCQ · 3.0 marks
Based on the above data, answer the given subquestions.
A published solution is not available for this question yet.
Question 17 MCQ · 2.0 marks
Based on the above data, answer the given subquestions.
Which of the following is the consensus of the motifs?
CTCTCA
TTTAAT
GGGACT
CCCTGA
A published solution is not available for this question yet.
Question 18 NAT · 3.0 marks
Based on the above data, answer the given subquestions.
A published solution is not available for this question yet.