bt4001_2026T2_Q1_NA.pdf

Algorithmic Thinking in Bioinformatics · Quiz 1 · May 2026

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

Question 2 MCQ · 3.0 marks

In a double-stranded DNA molecule, a researcher determines that **22%** of all bases (counting both strands together) are adenine (A). Recall that DNA obeys strict complementary base pairing: adenine (A) always pairs with thymine (T), and cytosine (C) always pairs with guanine (G). Using this constraint, what percentage of the total bases in the double-stranded molecule are guanine (G)?

A published solution is not available for this question yet.

Question 3 MCQ · 3.0 marks

Consider a hypothetical organism with exactly **4 genes**. Each gene can be in one of three states: OFF, ON at low expression, or ON at high expression. Assuming every combination of gene states defines a distinct cell type, how many theoretically possible cell types can this organism produce?

[[IMAGE:cafebd94349beeec_2_2]]
[[IMAGE:cafebd94349beeec_2_3]]
[[IMAGE:cafebd94349beeec_2_4]]
[[IMAGE:cafebd94349beeec_3_5]]

A published solution is not available for this question yet.

Question 4 MCQ · 3.0 marks

A researcher models a gene regulatory network among 4 genes (A, B, C, D) as a directed graph, where an edge from gene [[IMAGE:cafebd94349beeec_3_6]] to gene [[IMAGE:cafebd94349beeec_3_7]] means "gene [[IMAGE:cafebd94349beeec_3_8]] regulates gene [[IMAGE:cafebd94349beeec_3_9]] " (regardless of whether the regulation is activation or inhibition). The observed regulatory relationships are: • Gene A activates Gene B • Gene B activates Gene C • Gene C inhibits Gene A (forming a negative feedback loop) • Gene B activates Gene D • Gene C activates Gene D How many directed edges does this graph have, and how many genes have an in-degree of exactly 1?

5 edges; 3 genes have in-degree 1.
4 edges; 2 genes have in-degree 1.
5 edges; 2 genes have in-degree 1.
4 edges; 4 genes have in-degree 1.

A published solution is not available for this question yet.

Question 5 MCQ · 5.0 marks

Recall the color coding algorithm to compute a [[IMAGE:cafebd94349beeec_3_10]] -length path (connecting the regulators and receptors) with maximum weight. We had the following optimal substructure: [[IMAGE:cafebd94349beeec_3_11]] Consider a set of proteins [[IMAGE:cafebd94349beeec_4_12]] . You are asked to compute the path with maximum weight such that there are at least [[IMAGE:cafebd94349beeec_4_13]] and at most [[IMAGE:cafebd94349beeec_4_14]] proteins from [[IMAGE:cafebd94349beeec_4_15]] . To accommodate the same the DP matrix is modified as follows: Instead of a 2-D matrix, we use a 3-D DP matrix [[IMAGE:cafebd94349beeec_4_16]] such that [[IMAGE:cafebd94349beeec_4_17]] stores the maximum weight of a path of length [[IMAGE:cafebd94349beeec_4_18]] ending at [[IMAGE:cafebd94349beeec_4_19]] containing a vertex of each color in [[IMAGE:cafebd94349beeec_4_20]] and exactly [[IMAGE:cafebd94349beeec_4_21]] proteins from [[IMAGE:cafebd94349beeec_4_22]] . Which among the following is the correct optimal substructure for the algorithm?

[[IMAGE:cafebd94349beeec_4_23]]
[[IMAGE:cafebd94349beeec_4_24]]
[[IMAGE:cafebd94349beeec_4_25]]
[[IMAGE:cafebd94349beeec_4_26]]

A published solution is not available for this question yet.

Question 6 NAT · 3.0 marks

In a protein--protein interaction (PPI) study, a logistic regression model is trained to estimate the probability that two proteins truly interact, using three features computed for each protein pair [[IMAGE:cafebd94349beeec_5_27]] : • [[IMAGE:cafebd94349beeec_5_28]] : number of independent experimental studies that observed the interaction, • [[IMAGE:cafebd94349beeec_5_29]] : Pearson correlation of gene expression between the genes encoding [[IMAGE:cafebd94349beeec_5_30]] and [[IMAGE:cafebd94349beeec_5_31]] , • [[IMAGE:cafebd94349beeec_5_32]] : small-world clustering coefficient (fraction of shared interaction partners in the PPI network). The trained model is: [[IMAGE:cafebd94349beeec_5_33]] with learned parameters [[IMAGE:cafebd94349beeec_5_34]] , [[IMAGE:cafebd94349beeec_5_35]] , [[IMAGE:cafebd94349beeec_5_36]] , [[IMAGE:cafebd94349beeec_5_37]] . A protein pair [[IMAGE:cafebd94349beeec_5_38]] has feature values [[IMAGE:cafebd94349beeec_5_39]] ,; [[IMAGE:cafebd94349beeec_5_40]] ,; [[IMAGE:cafebd94349beeec_5_41]] . Compute the predicted interaction probability [[IMAGE:cafebd94349beeec_5_42]] . Enter the value correct to 2 decimal places.

A published solution is not available for this question yet.

Question 7 NAT · 3.0 marks

To discover signaling pathways in a yeast PPI network, researchers first estimate the probability of true interaction for each protein pair. They train a logistic regression model of the form: [[IMAGE:cafebd94349beeec_5_43]] where [[IMAGE:cafebd94349beeec_5_44]] is the number of independent high-throughput experiments (such as yeast two-hybrid or affinity purification--mass spectrometry studies) that detected the interaction, and [[IMAGE:cafebd94349beeec_6_45]] is the Pearson correlation of gene expression between the two proteins' encoding genes. For a particular protein pair, the gene expression correlation is [[IMAGE:cafebd94349beeec_6_46]] . What is the minimum integer value of [[IMAGE:cafebd94349beeec_6_47]] (the number of experimental studies) required so that the model considers the interaction more likely than not (i.e., [[IMAGE:cafebd94349beeec_6_48]] )? Enter the value as a single integer.

A published solution is not available for this question yet.

Question 8 NAT · 3.0 marks

After estimating interaction probabilities using logistic regression, the edge weight in a PPI graph is defined as [[IMAGE:cafebd94349beeec_6_49]] , so that path scores (sums of edge weights) correspond to log- probabilities. Consider a small PPI network with 5 proteins: [[IMAGE:cafebd94349beeec_6_50]] . The edge weights are: [[IMAGE:cafebd94349beeec_6_51]] Protein [[IMAGE:cafebd94349beeec_7_52]] is a membrane receptor and protein [[IMAGE:cafebd94349beeec_7_53]] is a transcription factor. A signaling pathway is modeled as a simple path (no repeated proteins) from [[IMAGE:cafebd94349beeec_7_54]] to [[IMAGE:cafebd94349beeec_7_55]] . What is the **score of the highest-scoring simple path** from [[IMAGE:cafebd94349beeec_7_56]] to [[IMAGE:cafebd94349beeec_7_57]] ? Enter the value as an integer.

A published solution is not available for this question yet.

Question 9 NAT · 4.0 marks

A receptor [[IMAGE:cafebd94349beeec_7_58]] receives information about a pathogen and transmits the information to gene [[IMAGE:cafebd94349beeec_7_59]] via the following edges. • [[IMAGE:cafebd94349beeec_7_60]] to [[IMAGE:cafebd94349beeec_7_61]] with edge probability [[IMAGE:cafebd94349beeec_7_62]] . • [[IMAGE:cafebd94349beeec_7_63]] to [[IMAGE:cafebd94349beeec_7_64]] with edge probability [[IMAGE:cafebd94349beeec_7_65]] . • [[IMAGE:cafebd94349beeec_7_66]] to [[IMAGE:cafebd94349beeec_7_67]] with edge probability [[IMAGE:cafebd94349beeec_7_68]] . • [[IMAGE:cafebd94349beeec_7_69]] to [[IMAGE:cafebd94349beeec_7_70]] with edge probability [[IMAGE:cafebd94349beeec_7_71]] . In a random coloring of the nodes of the underlying GRN network using [[IMAGE:cafebd94349beeec_7_72]] colors, what is the probability that this path is colorful? (Random coloring refers to coloring each node in the graph with one of the [[IMAGE:cafebd94349beeec_7_73]] colors uniformly and independently at random.) Round up the answer to 2 decimal points.

A published solution is not available for this question yet.

Question 10 NAT · 2.0 marks

You travel to an alien world where the DNAs are composed of a whopping [[IMAGE:cafebd94349beeec_8_74]] nucleotides, namely, [[IMAGE:cafebd94349beeec_8_75]] and are tasked with reading the gene [[IMAGE:cafebd94349beeec_8_76]] using two different machines. Let the noisy set of [[IMAGE:cafebd94349beeec_8_77]] -mer composition of [[IMAGE:cafebd94349beeec_8_78]] generated by the first machine is represented as [[IMAGE:cafebd94349beeec_8_79]] and the noisy set of [[IMAGE:cafebd94349beeec_8_80]] -mer composition of [[IMAGE:cafebd94349beeec_8_81]] generated by the second machine is represented as [[IMAGE:cafebd94349beeec_8_82]] . Note that, both of these compositions are generated by the machines, and thus, may contain missing and erroneous [[IMAGE:cafebd94349beeec_8_83]] -mers. Now, due to errors in the [[IMAGE:cafebd94349beeec_8_84]] -mers read by both machines, the sequence constructed from de Bruijn graph using [[IMAGE:cafebd94349beeec_8_85]] is BDACDDG and the sequence constructed from the overlap graph using [[IMAGE:cafebd94349beeec_8_86]] is FBFDEDDG. Answer the given subquestions with respect to the same.

What is the maximum possible out-degree of any node in the de Bruijn graph constructed using [[IMAGE:cafebd94349beeec_8_87]] ? Enter the value as a single integer.

A published solution is not available for this question yet.

Question 11 NAT · 4.0 marks

We say a position has been read correctly, if the nucleotide at that position in the optimal global alignment between the sequences are the same. Find the global alignment score with +1 scoring for a match and 0 penalty for mismatches and gaps, and hence, determine how many positions of the sequence have been read correctly. Enter the value as a single integer.

A published solution is not available for this question yet.

Question 12 NAT · 3.0 marks

How many [[IMAGE:cafebd94349beeec_9_88]] -mers were read by the second machine? Enter the value as a single integer.

A published solution is not available for this question yet.

Question 13 MCQ · 4.0 marks

Consider the sequence TTATTCGC, and answer the given subquestions on de Bruijn graphs constructed on the same sequence.

Consider the de Bruijn graph [[IMAGE:cafebd94349beeec_10_89]] constructed using the [[IMAGE:cafebd94349beeec_10_90]] -mer composition of the given sequence. Which of the following shows the correct number of nodes [[IMAGE:cafebd94349beeec_10_91]] and number of edges [[IMAGE:cafebd94349beeec_10_92]] in the graph?

[[IMAGE:cafebd94349beeec_10_93]]
[[IMAGE:cafebd94349beeec_10_94]]
[[IMAGE:cafebd94349beeec_10_95]]
[[IMAGE:cafebd94349beeec_10_96]]

A published solution is not available for this question yet.

Question 14 MCQ · 4.0 marks

Consider the sequence TTATTCGC, and answer the given subquestions on de Bruijn graphs constructed on the same sequence.

Consider the paired de Bruijn graph constructed using the [[IMAGE:cafebd94349beeec_10_97]] -composition of the given sequence i.e., the length of the [[IMAGE:cafebd94349beeec_10_98]] -mers [[IMAGE:cafebd94349beeec_10_99]] and the distance between the paired [[IMAGE:cafebd94349beeec_10_100]] -mers [[IMAGE:cafebd94349beeec_10_101]] . Which of the following shows the correct number of nodes [[IMAGE:cafebd94349beeec_10_102]] and number of edges [[IMAGE:cafebd94349beeec_10_103]] in the graph?

[[IMAGE:cafebd94349beeec_10_104]]
[[IMAGE:cafebd94349beeec_11_105]]
[[IMAGE:cafebd94349beeec_11_106]]
[[IMAGE:cafebd94349beeec_11_107]]

A published solution is not available for this question yet.

Question 15 NAT · 3.0 marks

Consider two input DNA sequences: [[IMAGE:cafebd94349beeec_11_108]] CAATGATC and [[IMAGE:cafebd94349beeec_11_109]] CCTGAATGC. Based on the above data, answer the given subquestions.

We would like to align [[IMAGE:cafebd94349beeec_11_110]] and [[IMAGE:cafebd94349beeec_11_111]] using the following score matrix (S). [[IMAGE:cafebd94349beeec_11_112]] What is the alignment score for the global alignment between the following two strings: [[IMAGE:cafebd94349beeec_11_113]] Enter the value as a single integer.

A published solution is not available for this question yet.

Question 16 MCQ · 3.0 marks

Consider two input DNA sequences: [[IMAGE:cafebd94349beeec_11_108]] CAATGATC and [[IMAGE:cafebd94349beeec_11_109]] CCTGAATGC. Based on the above data, answer the given subquestions.

Consider the global alignment between [[IMAGE:cafebd94349beeec_12_114]] and [[IMAGE:cafebd94349beeec_12_115]] . Let the score be computed as follows: [[IMAGE:cafebd94349beeec_12_116]] From the given options identify the highest-scoring global alignment(s) between the two strings ( [[IMAGE:cafebd94349beeec_12_117]] and [[IMAGE:cafebd94349beeec_12_118]] ).

[[IMAGE:cafebd94349beeec_12_119]]
[[IMAGE:cafebd94349beeec_12_120]]
[[IMAGE:cafebd94349beeec_12_121]]
[[IMAGE:cafebd94349beeec_12_122]]

A published solution is not available for this question yet.