Given a multiset of k-mers S_k, the pseudocode of the algorithm to construct the de Bruijn graph (G) is given below. Fill in the four blanks. multiset S_k = collection of input k-mers set S_{k-1} = ϕ for every i ∈ S_k add i[1, k − 1] and i[2, k] to set S_{k-1} for every i ∈ I add the node II to G for every i ∈ S_k add the edge from III to IV in G return G

(D) Option figure from the original question paper

(A) Option figure from the original question paper

(B) Option figure from the original question paper

(C) Option figure from the original question paper

May 2024 term · Algorithmic Thinking in Bioinformatics · BSBT4001

Algorithmic Thinking in Bioinformatics Quiz 1: 7 July 2024 (May 2024 term)

The IIT Madras BS Algorithmic Thinking in Bioinformatics (Algorithmic Thinking in Bioinformatics) Quiz 1 paper sat on 7 Jul 2024, in the May 2024 term: 15 questions for 50 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: 15
Marks: 50
Duration: 120 min
Numerical: 8
MCQ: 6
MSQ: 1

Take as mock test Practise with answers

Updated 25 Sept 2026

Official paper: IIT M DEGREE AN EXAM QDB2 7 July 2024 · No negative marking.

Question 1

+3 marksNumerical answer

Scientists found an alien world where life follows the same central dogma principle. Their DNA consists of 5 different types of nucleotides (and so is their RNA) and amino acids are generated using codons of length 4. Also, due to some chemical structure of the nucleotides, any nucleotide can occur exactly once in a codon. Calculate the maximum number of unique amino acids that be generated.
Enter the value as a single integer.

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Correct answer: 120

Question 1 on its own page

Question 2

+3 marksNumerical answer

Consider a GRN system with four genes: $g_1, g_2, g_3, g_4$ . The adjacency matrix that represents the GRN is given below. How many genes are regulating $g_4$ ?

	$g_2$	$g_3$	$g_4$
$g_1$	1	1	0
$g_2$	0	1	1
$g_3$	0	0	1
$g_4$	0	0	0

Table 1: The GRN network

Enter the value as a single integer.

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Correct answer: 2

Question 2 on its own page

Question 3

+3 marksNumerical answer

Show answer

Correct answer: 27

Question 3 on its own page

Question 4

+3 marksOne correct option

The figure below shows the genetic code describing the translation of an RNA codon into one of the twenty different amino acids. Use the figure below to answer the given subquestions.

Source: https://www.needpix.com/photo/93401/dna-amino-acids-biology-code-genetics- molecular-science

Find the translation of the following RNA string into an amino acid string.

A
TDTGL
B
TDTGF
C
TETGF
D
TETGL

Show answer

Correct answer

C
TETGF

Question 4 on its own page

Question 5

+3 marksNumerical answer

The figure below shows the genetic code describing the translation of an RNA codon into one of the twenty different amino acids. Use the figure below to answer the given subquestions.

Source: https://www.needpix.com/photo/93401/dna-amino-acids-biology-code-genetics- molecular-science

If the amino acid “Leucine (L)” is generated, then what is the probability that the codon encountered starts with “Uracil (U)”? Assume that the different positions of the codon are set to a nucleotide independently and uniformly at random.
Round your answer to two decimal digits.

Show answer

Correct answer: 0.33

Question 5 on its own page

Question 6

+3 marksNumerical answer

A receptor R receives information about a pathogen and transmits the information to gene G via the following edges.
• R to Y1 with edge probability 0.02.
• Y1 to Y2 with edge probability 0.03.
• Y2 to Y3 with edge probability 0.06.
• Y3 to G with edge probability 0.01.
Based on the above data, answer the given subquestions.

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Correct answer: 36

Question 6 on its own page

Question 7

+3 marksNumerical answer

In a random coloring of the nodes of the underlying GRN network using 6 colors, what is the probability that this path is colorful? (Random coloring refers to coloring each node in the graph with one of the 6 colors uniformly and independently at random.)
Round up the answer to 2 decimal points.

Show answer

Correct answer: 0.09

Question 7 on its own page

Question 8

+4 marksOne correct option

A potential cancer therapy drug "Y" was found to bind to certain cancer proteins in an experimental setup. Its binding efficiency (binding) was found to be based on its length (length), presence of $\beta$ -sheets (structure; $1 = \beta$ -sheet is present, $0 = \alpha$ -helix), and presence of hydrophobic side chains (HSC; $1 =$ side chains are hydrophobic, 0 otherwise). Using protein data from TCGA (a public database), logistic regression was performed to understand the drug behavior. The results are summarized below in a table. Compute the log odds of binding of drug "Y" for Protein C with 20 amino acids

	Coefficient	Standard error	Z	p-value
length	0.9	0.20	3.16	0.002
structure	0.3	0.77	2.73	0.006
HSC	2.5	0.26	1.99	0.047
constant	-25	3.28	-2.48	0.013

with $\alpha$ -helix structure and hydrophobic side chains and use the results to predict if this protein will bind or will not bind to the drug?

A
Yes, predicted to bind
B
No, not predicted to bind

Show answer

Correct answer

B
No, not predicted to bind

Question 8 on its own page

Question 9

+4 marksOne correct option

Given a multiset of $k$ -mers $S_k$ , the pseudocode of the algorithm to construct the de Bruijn graph (G) is given below. Fill in the four blanks.

text

1multiset S_k = collection of input k-mers
2set S_{k-1} = ϕ
3for every i ∈ S_k
4   add i[1, k − 1] and i[2, k] to set S_{k-1}
5for every i ∈ __I__
6   add the node __II__ to G
7for every i ∈ S_k
8   add the edge from __III__ to __IV__ in G
9return G

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Correct answer

Question 9 on its own page

Question 10

+3 marksOne correct option

In signaling pathway detection using the color coding algorithm, increasing the number of colors increases the probability of detecting the best scoring path, as well as the running time of each coloring run.

A
TRUE
B
FALSE

Show answer

Correct answer

A
TRUE

Question 10 on its own page

Question 11

+4 marksNumerical answer

The following reads are found from a genome sequence of some organism.
ATG,CAT, TAG,GAT, TTA,AAT,ATA, AGA, ATC, TGC,GCA
As a biologist, you have to assemble the sequence of the genome from these reads for your project. Answer the given subquestions with respect to the same. Recall that the Hamiltonian path approach is used in an overlap graph and the Eulerian path approach is used in the de Bruijn graph for the genome assembly problem.

How many nodes are there in the corresponding de Bruijn graph?
Enter the value as a single integer.

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Correct answer: 10

Question 11 on its own page

Question 12

+3 marksOne correct option

Which among the following statements is/are true?

A
The underlying genome can be constructed using both overlap and de Bruijn graphs.
B
The underlying genome can be constructed using overlap graph but not with de Bruijn graph.
C
The underlying genome can be constructed using de Bruijn graph but not with overlap graph.
D
The underlying genome cannot be constructed as certain reads are either missing or erroneous.

Show answer

Correct answer

D
The underlying genome cannot be constructed as certain reads are either missing or erroneous.

Question 12 on its own page

Question 13

+4 marksNumerical answer

Based on the above data, answer the given subquestions.

We would like to align $v$ and $w$ using the following score matrix (S).

	A	C	G	T	-
A	1	-3	-5	-1	-3
C	-4	1	-3	-2	-3
G	-9	-7	1	-1	-3
T	-3	-5	-8	1	-4
-	-4	-2	-2	-1

What is the alignment score for the global alignment between the following two strings:

-	G	-	-	T	T	A	C	T	A	G
G	G	A	C	T	T	A	C	-	-	G

Enter the value as a single integer.

Show answer

Correct answer: -9

Question 13 on its own page

Question 14

+4 marksOne correct option

Based on the above data, answer the given subquestions.

Consider the global alignment between v and w. Let the score be computed as follows:

From the given options identify the highest-scoring global alignment(s) between the two strings.

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Correct answer

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Question 15

+3 marksOne or more correct options

Which among the following statements is/are correct?

Select all that apply.

A
Global alignment involves aligning the entire sequences, while local alignment involves aligning smaller parts/substrings of the sequence.
B
Alignment problem can be solved using a greedy algorithm approach.
C
To compute the global alignment between two sequences, free rides (zero weight edges) are added from the source (0, 0) to every node and from every node to the sink (n, m) in the alignment graph.
D
The alignment problem can be solved in linear space.

Show answer

Correct answers

A
Global alignment involves aligning the entire sequences, while local alignment involves aligning smaller parts/substrings of the sequence.
D
The alignment problem can be solved in linear space.

Question 15 on its own page