The IIT Madras BS Algorithmic Thinking in Bioinformatics (Algorithmic Thinking in Bioinformatics) End Term paper sat on 30 Apr 2023, in the January 2023 term: 7 questions for 22 marks in 180 minutes. Every question is below with its answer. Take it as a timed mock test to be marked, or read it through first.
Many antibiotics interfere with the transfer of genetic information from X to Y, preventing bacteria from growing. Y is a polymer of Z. X has ribose sugar in its composition. Identify X, Y, and Z. Name the process that is affected by antibiotics here. X, Y, Z and the process are respectively:
RNA, Protein, Amino acids, Translation
DNA, Protein, Amino acids, Transcription
RNA, Protein, Amino acids, Transcription
RNA, Amino acids, Proteins, Translation
Correct answer
RNA, Protein, Amino acids, Translation
Sensitivity to outliers
Sensitivity to centroid initialization
Non-convergence
Some of the output clusters can be non-convex.
Correct answers
Non-convergence
Some of the output clusters can be non-convex.
Consider the following hypothetical phylogenetic tree constructed using viral sequences isolated from different host species.
Consider the following hypothetical phylogenetic tree constructed using viral sequences isolated from different host species.
Which of the following is/are true (with absolute certainty) with respect to the immediate common ancestor of the Human and Monkey viruses?
Human virus is the immediate common ancestor
Monkey virus is the immediate common ancestor
Goat virus is the immediate common ancestor
Cannot tell
Correct answer
Cannot tell
1
2
3
4
Correct answer
1
Which of the following statements is/are true?
1. UPGMA method builds a rooted phylogenetic tree while the neighbor-joining tree method builds an unrooted phylogenetic tree.
2. UPGMA algorithm requires the distances to be ultrametric while the neighbor-joining tree algorithm requires the distances to be additive, if we need to prove that the respective algorithm can correctly recover the true tree. 3. The basic assumption of the UPGMA method is that all taxa evolve at a constant rate and that they are equally distant from the root.
1 and 2
2 and 3
1 and 3
1, 2 and 3
Correct answer
1, 2 and 3
1 and 2
2 and 3
1 and 3
1, 2 and 3
Correct answer
1 and 2
Which of the following is/are true with respect to additive and ultrametric distance matrices and trees? Assume that the distance matrix satisfies the usual distance metric axioms like non-negativity, symmetricity and triangle inequality. Also, recall that an ultrametric distance matrix is any distance matrix that can be derived from some ultrametric tree (using the edge weights and paths in that tree).
A 3 × 3 non-additive distance matrix is possible.
A 4 × 4 non-additive distance matrix is possible.
All ultrametric distance matrices are additive but not vice-versa.
In an ultrametric tree, the distance from the root to any leaf is the same.
Correct answers
A 4 × 4 non-additive distance matrix is possible.
All ultrametric distance matrices are additive but not vice-versa.
In an ultrametric tree, the distance from the root to any leaf is the same.
