bt4001_2026T1_Q1_NA.pdf

Algorithmic Thinking in Bioinformatics · Quiz 1 · 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 · 4.0 marks

Given a multiset of [[IMAGE:4a1119e59f894ec3_3_2]] -mers [[IMAGE:4a1119e59f894ec3_3_3]] , the pseudocode of the algorithm to construct the de Bruijn graph (G) is given below. Fill in the four blanks. [[IMAGE:4a1119e59f894ec3_3_4]]

I: [[IMAGE:4a1119e59f894ec3_3_5]] , II: [[IMAGE:4a1119e59f894ec3_3_6]] , III: [[IMAGE:4a1119e59f894ec3_3_7]] , IV: [[IMAGE:4a1119e59f894ec3_3_8]]
I: [[IMAGE:4a1119e59f894ec3_3_9]] , II: [[IMAGE:4a1119e59f894ec3_3_10]] , III: [[IMAGE:4a1119e59f894ec3_3_11]] , IV: [[IMAGE:4a1119e59f894ec3_3_12]]
I: [[IMAGE:4a1119e59f894ec3_3_13]] , II: [[IMAGE:4a1119e59f894ec3_3_14]] , III: [[IMAGE:4a1119e59f894ec3_3_15]] , IV: [[IMAGE:4a1119e59f894ec3_3_16]]
I: [[IMAGE:4a1119e59f894ec3_3_17]] , II: [[IMAGE:4a1119e59f894ec3_3_18]] , III: [[IMAGE:4a1119e59f894ec3_3_19]] , IV: [[IMAGE:4a1119e59f894ec3_3_20]]

A published solution is not available for this question yet.

Question 3 MCQ · 3.0 marks

Consider the overlap graph representing all the connections between the following 3-mer collection: [[IMAGE:4a1119e59f894ec3_4_21]] . From among the given options, identify the string that can be constructed from some path in the overlap graph?

[[IMAGE:4a1119e59f894ec3_4_22]]
[[IMAGE:4a1119e59f894ec3_4_23]]
[[IMAGE:4a1119e59f894ec3_4_24]]
[[IMAGE:4a1119e59f894ec3_4_25]]

A published solution is not available for this question yet.

Question 4 MCQ · 3.0 marks

Consider a logistic regression model trained to predict whether a protein–protein interaction exists (interaction = 1, no interaction = 0) using two biological features in [[IMAGE:4a1119e59f894ec3_4_26]] (for example, expression correlation and functional similarity). The model predicts that the probability of interaction for the feature vector [[IMAGE:4a1119e59f894ec3_4_27]] is equal to [[IMAGE:4a1119e59f894ec3_4_28]] . What is the probability that a protein pair with feature vector [[IMAGE:4a1119e59f894ec3_4_29]] belongs to class [[IMAGE:4a1119e59f894ec3_5_30]] (interaction)?

[[IMAGE:4a1119e59f894ec3_5_31]]
[[IMAGE:4a1119e59f894ec3_5_32]]
[[IMAGE:4a1119e59f894ec3_5_33]]
[[IMAGE:4a1119e59f894ec3_5_34]]

A published solution is not available for this question yet.

Question 5 MCQ · 3.0 marks

Suppose we have a model that estimates the probability of a gene–disease association based on two features. Feature [[IMAGE:4a1119e59f894ec3_5_35]] represents the number of independent experimental studies supporting the association, and feature [[IMAGE:4a1119e59f894ec3_5_36]] represents the functional similarity between the gene and disease-related genes. Let [[IMAGE:4a1119e59f894ec3_5_37]] and [[IMAGE:4a1119e59f894ec3_5_38]] denote the weights corresponding to [[IMAGE:4a1119e59f894ec3_5_39]] and [[IMAGE:4a1119e59f894ec3_5_40]] respectively. Which of the following choices for [[IMAGE:4a1119e59f894ec3_5_41]] and [[IMAGE:4a1119e59f894ec3_5_42]] would be most appropriate to minimise the loss function?

[[IMAGE:4a1119e59f894ec3_5_43]]
[[IMAGE:4a1119e59f894ec3_5_44]]
[[IMAGE:4a1119e59f894ec3_5_45]]
[[IMAGE:4a1119e59f894ec3_5_46]]

A published solution is not available for this question yet.

Question 6 MSQ · 3.0 marks

Let [[IMAGE:4a1119e59f894ec3_6_47]] be a multiset of [[IMAGE:4a1119e59f894ec3_6_48]] -mers and [[IMAGE:4a1119e59f894ec3_6_49]] be the de Bruijn graph constructed from [[IMAGE:4a1119e59f894ec3_6_50]] . One of the [[IMAGE:4a1119e59f894ec3_6_51]] - mers [[IMAGE:4a1119e59f894ec3_6_52]] is replaced by another different [[IMAGE:4a1119e59f894ec3_6_53]] -mer [[IMAGE:4a1119e59f894ec3_6_54]] to obtain [[IMAGE:4a1119e59f894ec3_6_55]] , i.e., [[IMAGE:4a1119e59f894ec3_6_56]] and let the corresponding de Bruijn graph on [[IMAGE:4a1119e59f894ec3_6_57]] be [[IMAGE:4a1119e59f894ec3_6_58]] . If the node set of [[IMAGE:4a1119e59f894ec3_6_59]] and [[IMAGE:4a1119e59f894ec3_6_60]] remain the same, then the number of nodes with different degrees in the two graphs can be _______________________.

A published solution is not available for this question yet.

Question 7 MSQ · 3.0 marks

A logistic regression model has been trained to predict whether a gene pair interacts (interaction = 1, no interaction = 0) using two biological features (for example, co-expression score and shared pathway count). The feature vector for a test gene pair is [[IMAGE:4a1119e59f894ec3_6_61]] and the predicted probability of interaction using this trained logistic regression classifier turns out to be [[IMAGE:4a1119e59f894ec3_6_62]] Which of the following weight vectors could correspond to this logistic regression classifier? **Select** **all that apply.**

[[IMAGE:4a1119e59f894ec3_6_63]]
[[IMAGE:4a1119e59f894ec3_6_64]]
[[IMAGE:4a1119e59f894ec3_7_65]]
[[IMAGE:4a1119e59f894ec3_7_66]]

A published solution is not available for this question yet.

Question 8 MSQ · 5.0 marks

Consider two input DNA sequences: [[IMAGE:4a1119e59f894ec3_7_67]] [[IMAGE:4a1119e59f894ec3_7_68]] and [[IMAGE:4a1119e59f894ec3_7_69]] [[IMAGE:4a1119e59f894ec3_7_70]] . Consider an alignment game to align [[IMAGE:4a1119e59f894ec3_7_71]] and [[IMAGE:4a1119e59f894ec3_7_72]] such that we can score the maximum number of points. Scoring is done as follows: • For each match between two symbols: +1 point • For each mismatch between two symbols: 0 point • For each removal of symbol from any one sequence: 0 point Which of the following alignment(s) between the two strings scores the highest point?

[[IMAGE:4a1119e59f894ec3_7_73]]
[[IMAGE:4a1119e59f894ec3_7_74]]
[[IMAGE:4a1119e59f894ec3_7_75]]
[[IMAGE:4a1119e59f894ec3_7_76]]

A published solution is not available for this question yet.

Question 9 NAT · 3.0 marks

Suppose you fly to an alien world and are surprised to find that life there follows the same central dogma. The difference is that the alien life has 3 distinct nucleotides that make up DNA sequences and a whopping [[IMAGE:4a1119e59f894ec3_8_77]] distinct amino acids that make up protein sequences. What is the minimum length of each codon in this alien species? Enter your answer as a single integer.

A published solution is not available for this question yet.

Question 10 NAT · 3.0 marks

Suppose [[IMAGE:4a1119e59f894ec3_8_78]] is the composition of the DNA string [[IMAGE:4a1119e59f894ec3_8_79]] . If the overlap graph constructed on [[IMAGE:4a1119e59f894ec3_8_80]] has [[IMAGE:4a1119e59f894ec3_8_81]] nodes, then what is the length of [[IMAGE:4a1119e59f894ec3_8_82]] ? Enter the value as a single integer.

A published solution is not available for this question yet.

Question 11 MCQ · 3.0 marks

Consider the GRN system with four genes: [[IMAGE:4a1119e59f894ec3_8_83]] and [[IMAGE:4a1119e59f894ec3_8_84]] given in the following figure. Answer the given subquestions with respect to the same. [[IMAGE:4a1119e59f894ec3_9_85]]

Which of the following is the correct adjacency matrix for the same?

[[IMAGE:4a1119e59f894ec3_9_86]]
[[IMAGE:4a1119e59f894ec3_9_87]]
[[IMAGE:4a1119e59f894ec3_9_88]]
[[IMAGE:4a1119e59f894ec3_9_89]]

A published solution is not available for this question yet.

Question 12 MSQ · 3.0 marks

Which of the following statement/s correctly represent the relationship among the genes? Consider both single-hop and multi-hop influences of one gene on another.

[[IMAGE:4a1119e59f894ec3_10_90]] regulates all the other three genes.
[[IMAGE:4a1119e59f894ec3_10_91]] regulates only [[IMAGE:4a1119e59f894ec3_10_92]] and [[IMAGE:4a1119e59f894ec3_10_93]] but not [[IMAGE:4a1119e59f894ec3_10_94]] .
[[IMAGE:4a1119e59f894ec3_10_95]] regulates [[IMAGE:4a1119e59f894ec3_10_96]] and [[IMAGE:4a1119e59f894ec3_10_97]] .
[[IMAGE:4a1119e59f894ec3_10_98]] is regulated by all the other three genes.

A published solution is not available for this question yet.

Question 13 NAT · 3.0 marks

A receptor [[IMAGE:4a1119e59f894ec3_10_99]] receives information about a pathogen and transmits the information to gene [[IMAGE:4a1119e59f894ec3_10_100]] via the following edges. • [[IMAGE:4a1119e59f894ec3_10_101]] to [[IMAGE:4a1119e59f894ec3_10_102]] with edge probability [[IMAGE:4a1119e59f894ec3_10_103]] . • [[IMAGE:4a1119e59f894ec3_10_104]] to [[IMAGE:4a1119e59f894ec3_10_105]] with edge probability [[IMAGE:4a1119e59f894ec3_10_106]] . • [[IMAGE:4a1119e59f894ec3_10_107]] to [[IMAGE:4a1119e59f894ec3_10_108]] with edge probability [[IMAGE:4a1119e59f894ec3_10_109]] . • [[IMAGE:4a1119e59f894ec3_10_110]] to [[IMAGE:4a1119e59f894ec3_10_111]] with edge probability [[IMAGE:4a1119e59f894ec3_10_112]] . Answer the given subquestions with respect to the same.

If the probability that the information has transmitted along the path is represented as [[IMAGE:4a1119e59f894ec3_10_113]] , then calculate the value of [[IMAGE:4a1119e59f894ec3_10_114]] . Assume that the transmission events along these edges are mutually independent. Enter the value as a single integer.

A published solution is not available for this question yet.

Question 14 NAT · 3.0 marks

In a random coloring of the nodes of the underlying GRN network using [[IMAGE:4a1119e59f894ec3_11_115]] 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:4a1119e59f894ec3_11_116]] 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 15 NAT · 5.0 marks

Given below in figure is the BLOSUM50 scoring matrix for amino acids. Use the same as the scoring matrix and answer the given subquestions. [[IMAGE:4a1119e59f894ec3_12_117]]

The peptide MSTWPQ is aligned with the peptide generated from the RNA string AUGCCUCAA. If gap opening penalty is -20 and gap extension penalty is -2, then use the genetic code given below to compute the optimal global alignment score between the peptides. [[IMAGE:4a1119e59f894ec3_13_118]]

A published solution is not available for this question yet.

Question 16 NAT · 3.0 marks

Given below in figure is the BLOSUM50 scoring matrix for amino acids. Use the same as the scoring matrix and answer the given subquestions. [[IMAGE:4a1119e59f894ec3_12_117]]

Calculate the local alignment score between the same two peptides as in the previous question.

A published solution is not available for this question yet.