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January 2023 term · Algorithmic Thinking in Bioinformatics · BSBT4001

Algorithmic Thinking in Bioinformatics Quiz 2: 2 April 2023, Set QPE2 (January 2023 term)

The IIT Madras BS Algorithmic Thinking in Bioinformatics (Algorithmic Thinking in Bioinformatics) Quiz 2 paper sat on 2 Apr 2023, in the January 2023 term, set QPE2: 10 questions for 37 marks in 120 minutes. Every question is below with its answer. Take it as a timed mock test to be marked, or read it through first.

Questions
10
Marks
37
Duration
120 min
Numerical
1
MSQ
1
MCQ
8
Take as mock testPractise with answers

Updated

Official paper: IIT M DEGREE AN3 EXAM QPE3 02 Apr 2023 · No negative marking.

Question 1

+4 marksNumerical answer

You enter an alien world as a renowned computational biologist. The below table is presented to you as a part of a preliminary study done by a group of scientists to study the local fauna around the base camp. They analyze the DNA and figure out that there are only two bases “+” and “0”. The below table represents the DNA sequence in 6 positions for the different species found. You build a phylogenetic tree that best represents the evolutionary relationship among the species, using the Neighbor-Joining algorithm (on the Hamming distance matrix).

You enter an alien world as a renowned computational biologist. The below table is presented to you as a part of a preliminary study done by a group of scientists to study the local fauna around the base camp. They analyze the DNA and figure out that there are only two bases “+” and “0”. The below table represents the DNA sequence in 6 positions for the different species found. You build a phylogenetic tree that best represents the evolutionary relationship among the species, using the Neighbor-Joining algorithm (on the Hamming distance matrix).
Based on the above data, answer the given subquestions

The length or weight of the internal edge (i.e., non-limb edge) in the inferred phylogenetic tree is____________ . Fill in the blank.

Show answer

Correct answer: 2

Question 1 on its own page

Question 2

+3 marksOne or more correct options

You enter an alien world as a renowned computational biologist. The below table is presented to you as a part of a preliminary study done by a group of scientists to study the local fauna around the base camp. They analyze the DNA and figure out that there are only two bases “+” and “0”. The below table represents the DNA sequence in 6 positions for the different species found. You build a phylogenetic tree that best represents the evolutionary relationship among the species, using the Neighbor-Joining algorithm (on the Hamming distance matrix).

You enter an alien world as a renowned computational biologist. The below table is presented to you as a part of a preliminary study done by a group of scientists to study the local fauna around the base camp. They analyze the DNA and figure out that there are only two bases “+” and “0”. The below table represents the DNA sequence in 6 positions for the different species found. You build a phylogenetic tree that best represents the evolutionary relationship among the species, using the Neighbor-Joining algorithm (on the Hamming distance matrix).
Based on the above data, answer the given subquestions

Consider the two distance matrices DM1 and DM2 shown below. Which of the following statement(s) is/are true?

Consider the two distance matrices DM1 and DM2 shown below. Which of the following statement(s) is/are true?

Select all that apply.

  1. A

    DM1 is additive, and DM2 is additive.

  2. B

    DM1, but not DM2 is additive

  3. C

    There exists an ultrametric tree that fits DM1, but not DM2.

  4. D

    There exists an ultrametric tree that fits DM2, but not DM1.

Show answer

Correct answers

  • A

    DM1 is additive, and DM2 is additive.

  • D

    There exists an ultrametric tree that fits DM2, but not DM1.

Question 2 on its own page

Question 3

+2 marksOne correct option

Which of the following is/are false about UPGMA?

  1. A

    UPGMA is a simple clustering heuristic that proceeds via iterative pairwisegrouping in each step.

  2. B

    Given a distance matrix, it starts by grouping two taxa with the largestpairwise distance in the distance matrix.

  3. C

    The distances between this new composite taxon and all remaining taxa arecalculated to create a reduced matrix.

  4. D

    The grouping process is repeated and another newly reduced matrix iscreated.

Show answer

Correct answer

  • B

    Given a distance matrix, it starts by grouping two taxa with the largestpairwise distance in the distance matrix.

Question 3 on its own pageAlso asked in Quiz 2 2 Apr 2023

Question 4

+5 marksOne correct option

Given below are a set of genetic sequences and the position (sites) of their nucleotides.

Given below are a set of genetic sequences and the position (sites) of their nucleotides.
Based on the above data, answer the given subquestions.

You are asked to construct a rooted binary phylogenetic tree from the given data. You identify 3 tree configurations that are possible - Tree A, Tree B, and Tree C (see the figure below) based on the information. Identify the most parsimonious tree. (HINT: Which columns can you ignore?)

You are asked to construct a rooted binary phylogenetic tree from the given data. You identify 3 tree configurations that are possible - Tree A, Tree B, and Tree C (see the figure below) based on the information. Identify the most parsimonious tree. (HINT: Which columns can you ignore?)

  1. A

    Tree A and B

  2. B

    Only Tree B

  3. C

    Tree A and C

  4. D

    Only Tree C

Show answer

Correct answer

  • B

    Only Tree B

Question 4 on its own page

Question 5

+3 marksOne correct option

Given below are a set of genetic sequences and the position (sites) of their nucleotides.

Given below are a set of genetic sequences and the position (sites) of their nucleotides.
Based on the above data, answer the given subquestions.

You add 4 more sequences to this tree. How many internal nodes and branches will the modified tree have?

  1. A

    7 internal nodes and 12 branches

  2. B

    7 internal nodes and 14 branches

  3. C

    8 internal nodes and 14 branches

  4. D

    8 internal nodes and 16 branches

Show answer

Correct answer

  • B

    7 internal nodes and 14 branches

Question 5 on its own page

Question 6

+4 marksOne correct option

Answer the given subquestions.

  1. A

    34

  2. B

    33

  3. C

    32

  4. D

    35

Show answer

Correct answer

  • C

    32

Question 6 on its own page

Question 7

+4 marksOne correct option

Answer the given subquestions.

Find the number of edges in the suffix tree constructed from the suffix trie obtained in the previous question.

  1. A

    11

  2. B

    10

  3. C

    20

  4. D

    28

Show answer

Correct answer

  • B

    10

Question 7 on its own page

Question 8

+4 marksOne correct option
  1. A

    GCCT

  2. B

    GTCC

  3. C

    TGCC

  4. D

    Reconstruction is not possible.

Show answer

Correct answer

  • A

    GCCT

Question 8 on its own page

Question 9

+3 marksOne correct option

Select the correct sequence of steps in the context of the K-means clustering algorithm:
I. Measurement of distances of each point to centroids. II. Initialization of cluster centroids. III. Updation of cluster centroids, and repeat. IV. Assignment of data points to respective clusters.

  1. A

    I, II, III, IV

  2. B

    II, I, IV, III

  3. C

    IV, III, II, I

  4. D

    II, I, III, IV

Show answer

Correct answer

  • B

    II, I, IV, III

Question 9 on its own pageAlso asked in Quiz 2 2 Apr 2023

Question 10

+5 marksOne correct option

Answer the given subquestions.

Consider the following hard K-means clustering problem with four points: P (1, 1), Q (2, 1), R (4, 3), and S (5, 4). Consider the number of clusters to be k = 2 and the initial centroids to be C1 = (0, 0) and C2 = (4, 4). After how many iterations will the algorithm terminate and what will be the final centroids?

  1. A

    2, (1, 1), (4, 4)

  2. B

    3, (1, 1), (4, 4)

  3. C

    4, (1.5, 1), (4.5, 3.5)

  4. D

    2, (1.5, 1), (4.5, 3.5)

Show answer

Correct answer

  • D

    2, (1.5, 1), (4.5, 3.5)

Question 10 on its own pageAlso asked in Quiz 2 2 Apr 2023