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bt4001_2025T1_Q1_NA.pdf

Algorithmic Thinking in Bioinformatics · Quiz 1 · Jan 2025

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Question 2 MCQ · 3.0 marks

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A published solution is not available for this question yet.

Question 3 NAT · 3.0 marks

Calculate the optimal global alignment score for the DNA sequences GAATTC and GATTA. Scoring is done as follows: • For every match: +2 points • For every mismatch: -1 points • For every insertion or deletion: -2 points

    A published solution is not available for this question yet.

    Question 4 NAT · 3.0 marks

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      A published solution is not available for this question yet.

      Question 5 NAT · 4.0 marks

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        A published solution is not available for this question yet.

        Question 6 NAT · 5.0 marks

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          A published solution is not available for this question yet.

          Question 7 MSQ · 3.0 marks

          The figure below shows the genetic code describing the translation of an RNA codon into one of the twenty different amino acids. Use the figure below to answer the given subquestions. [[IMAGE:b14f94f5b7581ae4_5_8]]
          A protein “X” has only three amino acids – “Serine”, “Leucine” and “Valine” in the same order. Which of the following RNA strings translate into the protein “X”?
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          1. CUC AGUGU A
          2. CUUUUGAGCGUUGUU
          3. AGUCUCGU A
          4. UC AUU AGUG
          5. UCGUUGGUU

          A published solution is not available for this question yet.

          Question 8 NAT · 3.0 marks

          The figure below shows the genetic code describing the translation of an RNA codon into one of the twenty different amino acids. Use the figure below to answer the given subquestions. [[IMAGE:b14f94f5b7581ae4_5_8]]
          What is the probability that a random RNA sequence of length 3 encodes for the “Arginine” amino acid? Assume that the different positions of the 3-mer RNA sequence are set to a nucleotide independently and uniformly at random.
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            A published solution is not available for this question yet.

            Question 9 NAT · 3.0 marks

            The figure below shows the genetic code describing the translation of an RNA codon into one of the twenty different amino acids. Use the figure below to answer the given subquestions. [[IMAGE:b14f94f5b7581ae4_5_8]]
            Suppose protein X consists of 3 amino acids. What is the maximum number of possible mRNA sequences that can generate the protein X?
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              A published solution is not available for this question yet.

              Question 10 NAT · 3.0 marks

              Consider the following cell signaling network and answer the given subquestions with respect to the same. Please note that the weight we written next to each edge e is the probability of (information flow through) this edge, and that the probability (or score) of a path is calculated under the assumption that the information flow through different edges are independent of each other. [[IMAGE:b14f94f5b7581ae4_7_9]]
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                A published solution is not available for this question yet.

                Question 11 MCQ · 3.0 marks

                Consider the following cell signaling network and answer the given subquestions with respect to the same. Please note that the weight we written next to each edge e is the probability of (information flow through) this edge, and that the probability (or score) of a path is calculated under the assumption that the information flow through different edges are independent of each other. [[IMAGE:b14f94f5b7581ae4_7_9]]
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                1. YES
                2. NO

                A published solution is not available for this question yet.

                Question 12 NAT · 3.0 marks

                Consider the following cell signaling network and answer the given subquestions with respect to the same. Please note that the weight we written next to each edge e is the probability of (information flow through) this edge, and that the probability (or score) of a path is calculated under the assumption that the information flow through different edges are independent of each other. [[IMAGE:b14f94f5b7581ae4_7_9]]
                In a random coloring of the path Ra, X1, Y1, Z1, G1 using 6 colors, what is the probability that this path is colorful? (Random coloring refers to coloring each node in the graph with one of the 6 colors uniformly and independently at random.)
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                  A published solution is not available for this question yet.

                  Question 13 MSQ · 3.0 marks

                  Answer the given subquestions about the graphs given below regarding overlap and de Bruijn graphs. Recall that the Hamiltonian path approach is used in an overlap graph and the Eulerian path approach is used in the de Bruijn graph for the genome assembly problem. (Hint: Be careful with the direction of the arrows.) [[IMAGE:b14f94f5b7581ae4_9_12]]
                  Which of the given graphs can be the overlap graph representing all k-mers of a string representing some linear (non-circular) genome?
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                  1. Graph 1
                  2. Graph 2
                  3. Graph 3

                  A published solution is not available for this question yet.

                  Question 14 MCQ · 3.0 marks

                  Answer the given subquestions about the graphs given below regarding overlap and de Bruijn graphs. Recall that the Hamiltonian path approach is used in an overlap graph and the Eulerian path approach is used in the de Bruijn graph for the genome assembly problem. (Hint: Be careful with the direction of the arrows.) [[IMAGE:b14f94f5b7581ae4_9_12]]
                  Which of the given graphs can be the de Bruijn graph representing all k-mers of a string representing some linear (non-circular) genome?
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                  1. Graph 1
                  2. Graph 2
                  3. Graph 3

                  A published solution is not available for this question yet.

                  Question 15 NAT · 2.0 marks

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                    A published solution is not available for this question yet.

                    Question 16 NAT · 2.0 marks

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                    Suppose we compute the score using the score matrix (S). What is the difference in the alignment score for the two global alignments? Enter the value as a single integer.
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                      A published solution is not available for this question yet.

                      Question 17 NAT · 4.0 marks

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                        A published solution is not available for this question yet.