bt4001_2026T1_Q2_NA.pdf

Algorithmic Thinking in Bioinformatics · Quiz 2 · Jan 2026

Questions and published explanations below are available without starting a test. Some questions may not have a published solution yet.

Question 2 MCQ · 2.0 marks

Which of the following statements is false about UPGMA?

UPGMA is a simple clustering heuristic that proceeds via iterative pairwise grouping in each step.
Given a distance matrix, it starts by grouping two taxa with the largest pairwise distance in the distance matrix.
The distances between this new composite taxon and all remaining taxa are calculated to create a reduced matrix.
The grouping process is repeated and another newly reduced matrix is created.

A published solution is not available for this question yet.

Question 3 MCQ · 3.0 marks

For some string [[IMAGE:98b4ab1b62d07a9c_2_2]] we have [[IMAGE:98b4ab1b62d07a9c_2_3]] . Which of the following represents the original string [[IMAGE:98b4ab1b62d07a9c_2_4]] ?

[[IMAGE:98b4ab1b62d07a9c_2_5]]
[[IMAGE:98b4ab1b62d07a9c_2_6]]
[[IMAGE:98b4ab1b62d07a9c_3_7]]
[[IMAGE:98b4ab1b62d07a9c_3_8]]

A published solution is not available for this question yet.

Question 4 MCQ · 5.0 marks

In a gene expression analysis study, we are clustering cells based on their expression levels of two genes using **(vanilla) soft K-means clustering**. The stiffness parameter is [[IMAGE:98b4ab1b62d07a9c_3_9]] . In the first iteration, suppose the cluster centroids represent two **cell types** with mean gene expression profiles: [[IMAGE:98b4ab1b62d07a9c_3_10]] Now consider a new cell [[IMAGE:98b4ab1b62d07a9c_3_11]] , where the coordinates represent its expression levels of the two genes. Which of the following options correctly represents the responsibilities (soft cluster memberships) of cell [[IMAGE:98b4ab1b62d07a9c_3_12]] belonging to cell types [[IMAGE:98b4ab1b62d07a9c_3_13]] and [[IMAGE:98b4ab1b62d07a9c_3_14]] ?

[[IMAGE:98b4ab1b62d07a9c_3_15]]
[[IMAGE:98b4ab1b62d07a9c_3_16]]
[[IMAGE:98b4ab1b62d07a9c_3_17]]
[[IMAGE:98b4ab1b62d07a9c_3_18]]

A published solution is not available for this question yet.

Question 5 MCQ · 5.0 marks

Consider the following hard K-means clustering problem with five points: [[IMAGE:98b4ab1b62d07a9c_3_19]] , [[IMAGE:98b4ab1b62d07a9c_3_20]] , [[IMAGE:98b4ab1b62d07a9c_3_21]] , [[IMAGE:98b4ab1b62d07a9c_3_22]] , and [[IMAGE:98b4ab1b62d07a9c_3_23]] . The number of clusters is [[IMAGE:98b4ab1b62d07a9c_4_24]] , and the initial centroids are [[IMAGE:98b4ab1b62d07a9c_4_25]] and [[IMAGE:98b4ab1b62d07a9c_4_26]] . After how many iterations will the algorithm terminate, and what will be the final centroids?

[[IMAGE:98b4ab1b62d07a9c_4_27]]
[[IMAGE:98b4ab1b62d07a9c_4_28]]
[[IMAGE:98b4ab1b62d07a9c_4_29]]
[[IMAGE:98b4ab1b62d07a9c_4_30]]

A published solution is not available for this question yet.

Question 6 NAT · 5.0 marks

What is the number of nodes in the **suffix trie** constructed on the genome: [[IMAGE:98b4ab1b62d07a9c_4_31]] . Assume the branch on the single-letter suffix [[IMAGE:98b4ab1b62d07a9c_4_32]] is not represented in this trie. Enter your answer as a single integer.

A published solution is not available for this question yet.

Question 7 NAT · 5.0 marks

Consider a clustering setup with [[IMAGE:98b4ab1b62d07a9c_4_33]] clusters. One cluster center has already been fixed at [[IMAGE:98b4ab1b62d07a9c_4_34]] . We now wish to select the second cluster center from the remaining points [[IMAGE:98b4ab1b62d07a9c_4_35]] . In order to encourage diversity between clusters, points that are farther from the existing center are given higher preference. Specifically, each point is assigned a selection probability proportional to the square of its distance from the nearest existing center (similar to a soft assignment where distant points receive higher weight). The Euclidean distances of the remaining points from [[IMAGE:98b4ab1b62d07a9c_5_36]] are: [[IMAGE:98b4ab1b62d07a9c_5_37]] What is the probability of selecting [[IMAGE:98b4ab1b62d07a9c_5_38]] as the second cluster center under this distance-based soft selection scheme? Round your answer to two decimal digits.

A published solution is not available for this question yet.

Question 8 NAT · 2.0 marks

The number of elements in the Burrows-Wheeler matrix is [[IMAGE:98b4ab1b62d07a9c_5_39]] . What is the length of the original genome sequence (including the [[IMAGE:98b4ab1b62d07a9c_5_40]] symbol)? Enter the value as a single integer.

A published solution is not available for this question yet.

Question 9 NAT · 2.0 marks

What is the minimum possible length of the run-length encoding of a genome sequence of length [[IMAGE:98b4ab1b62d07a9c_6_41]] . (Hint: Beware that the length of a run-length encoding of a string should include the characters in the encoded string, as well as their counts.) Enter the value as a single integer.

A published solution is not available for this question yet.

Question 10 NAT · 3.0 marks

You enter an alien world as a renowned computational biologist and discover five different species. The distance matrix among these species is provided below. [[IMAGE:98b4ab1b62d07a9c_6_42]] Now, to construct the phylogeny on these species, you apply the Neighbor-Joining algorithm and generate the following [[IMAGE:98b4ab1b62d07a9c_6_43]] matrix. [[IMAGE:98b4ab1b62d07a9c_7_44]] Answer the given sub-questions based on the same.

[[IMAGE:98b4ab1b62d07a9c_7_45]] ________________________. Enter the value as a single integer.

A published solution is not available for this question yet.

Question 11 NAT · 3.0 marks

[[IMAGE:98b4ab1b62d07a9c_7_46]] _____________________. Enter the value as a single integer.

A published solution is not available for this question yet.

Question 12 NAT · 3.0 marks

[[IMAGE:98b4ab1b62d07a9c_8_47]] ______________________. Enter the value as a single integer.

A published solution is not available for this question yet.

Question 13 MCQ · 1.0 marks

Which of the following species forms a cherry in the resulting phylogeny?

B and A
B and D
B and E
B and C

A published solution is not available for this question yet.

Question 14 MCQ · 2.0 marks

Given below is the profile matrix for a set of [[IMAGE:98b4ab1b62d07a9c_8_48]] motifs [[IMAGE:98b4ab1b62d07a9c_8_49]] . [[IMAGE:98b4ab1b62d07a9c_8_50]] . [[IMAGE:98b4ab1b62d07a9c_8_51]] Answer the given sub-questions with respect to the same.

Find the consensus of the motifs?