Algorithmic Thinking in Bioinformatics · End Term · May 2024 · AN

In an alien world, mutations occur in every 10 million years only. A ultrametric tree is constructed on some of these alien species. If the height of the tree (defined as the maximum number of edges from the root to a leaf node in the tree) is 5, then calculate the age of the root node (in million years) of this ultrametric tree. (Hint: The distance between two nodes in consecutive levels is given in the question.)

What is the number of free parameters that are learned in the EM setup of motif finding problem with an assumption of motif of length 5?

Which of the following statements about the EM algorithm is/are FALSE?

You are studying the signalling pathway system of an alien world. Existing literature shows that information in the alien world is transmitted in the following procedure. “A receptor protein in the cell membrane transmits information to a series of three kinase proteins that are sequentially activated inside the cell. The final activated kinase causes a transcription factor (TF) to get activated and translocated to the nucleus, wherein the TF protein regulates a target gene.” As part of your research, you construct the underlying signalling network, and want to find the most probable pathway along which a specific gene g will receive the information from a receptor on the cell membrane. Will it suffice to use 10 colors to determine the most probable pathway?

The de Bruijn graph of some linear (i.e., non-circular) genome Dna comprises of 2 nodes (N1 and N2) and 6 edges – three of these edges are directed from N1 to N2 and the remaining three edges are directed from N2 to N1. To reconstruct Dna, you are allowed to start only from the node N1. Answer the given subquestions with respect to the same.

Suppose you don’t know the 2-mers representing N1 and N2. Then which of the following is/are possible choices for Dna?

The de Bruijn graph of some linear (i.e., non-circular) genome Dna comprises of 2 nodes (N1 and N2) and 6 edges – three of these edges are directed from N1 to N2 and the remaining three edges are directed from N2 to N1. To reconstruct Dna, you are allowed to start only from the node N1. Answer the given subquestions with respect to the same.

Which of the following statements is/are correct? I. If we are allowed to start from N1 node only and the k-mers represented by both N1 and N2 are fixed, then there is exactly one genome sequence that can be reconstructed from this de Bruijn graph. II. If we are allowed to start from either node and the k-mers represented by both N1 and N2 are fixed, then there are exactly two genome sequences that can be reconstructed from this de Bruijn graph.

Based on the above data, answer the given subquestions.

Which of the following options is the original message?

Based on the above data, answer the given subquestions.

Choose the option representing the original suffix array of the message.