Algorithmic Thinking in Bioinformatics Quiz 1: 15 March 2026 (January 2026 term)

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

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

Consider a logistic regression model trained to predict whether a protein–protein interaction exists (interaction = 1, no interaction = 0) using two biological features in (for example, expression correlation and functional similarity). The model predicts that the probability of interaction for the feature vector

is equal to . What is the probability that a protein pair with feature vector

belongs to class (interaction)?

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

Let be a multiset of -mers and be the de Bruijn graph constructed from . One of the - mers is replaced by another different -mer to obtain , i.e., and let the corresponding de Bruijn graph on be . If the node set of and remain the same, then the number of nodes with different degrees in the two graphs can be _______________________.

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

and the predicted probability of interaction using this trained logistic regression classifier turns out to be

Which of the following weight vectors could correspond to this logistic regression classifier? Select all that apply.

Consider two input DNA sequences: and . Consider an alignment game to align and 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?

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 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.

Suppose is the composition of the DNA string . If the overlap graph constructed on has nodes, then what is the length of ? Enter the value as a single integer.

Consider the GRN system with four genes: and given in the following figure. Answer the given subquestions with respect to the same.

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

Consider the GRN system with four genes: and given in the following figure. Answer the given subquestions with respect to the same.

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.

A receptor receives information about a pathogen and transmits the information to gene via the following edges. • to with edge probability . • to with edge probability . • to with edge probability . • to with edge probability . Answer the given subquestions with respect to the same.

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

A receptor receives information about a pathogen and transmits the information to gene via the following edges. • to with edge probability . • to with edge probability . • to with edge probability . • to with edge probability . Answer the given subquestions with respect to the same.

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

Given below in figure is the BLOSUM50 scoring matrix for amino acids. Use the same as the scoring matrix and answer the given subquestions.

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.

Given below in figure is the BLOSUM50 scoring matrix for amino acids. Use the same as the scoring matrix and answer the given subquestions.

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

Consider the GRN system with four genes: and given in the following figure. Answer the given subquestions with respect to the same.

A receptor receives information about a pathogen and transmits the information to gene via the following edges. • to with edge probability . • to with edge probability . • to with edge probability . • to with edge probability . Answer the given subquestions with respect to the same.

Given below in figure is the BLOSUM50 scoring matrix for amino acids. Use the same as the scoring matrix and answer the given subquestions.