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bt4001_2025T2_Q1_NA.pdf

Algorithmic Thinking in Bioinformatics · Quiz 1 · May 2025

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Question 2 NAT · 4.0 marks

[[IMAGE:ece6cb607d1eeb32_3_0]]
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    A published solution is not available for this question yet.

    Question 3 NAT · 5.0 marks

    [[IMAGE:ece6cb607d1eeb32_4_1]]
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      Question 4 MCQ · 2.0 marks

      [[IMAGE:ece6cb607d1eeb32_4_2]]
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      1. reduces by about 50.
      2. increases by about 2.
      3. increases by about 0.7.
      4. does not change.

      A published solution is not available for this question yet.

      Question 5 MSQ · 3.0 marks

      [[IMAGE:ece6cb607d1eeb32_5_3]]
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      1. 0
      2. 1
      3. 2
      4. 3
      5. 4

      A published solution is not available for this question yet.

      Question 6 MSQ · 2.0 marks

      You are given a multiset of k-mers A based on a sequencing experiment and you want to reconstruct a genome sequence S whose k-mer composition is consistent with A. Let Go and Gd respectively denote the overlap and de Bruijn graph constructed using A. Which of the following statements is/are true?
      1. If a Hamiltonian path corresponding to S exists in Go, then an Eulerian path corresponding to S exists in Gd.
      2. If an Eulerian path corresponding to S exists in Gd, then a Hamiltonian path corresponding to S exists in Go.
      3. If a Hamiltonian path corresponding to S does not exist in Go, then an Eulerian path corresponding to S does not exist in Gd.
      4. If an Eulerian path corresponding to S does not exist in Gd, then a Hamiltonian path corresponding to S does not exist in Go.

      A published solution is not available for this question yet.

      Question 7 MCQ · 1.0 marks

      You fly to an alien world and are surprised to find life that follows the same central dogma principle. The difference is that the alien life has 5 different nucleotides. Answer the given subquestions with respect to the same.
      Suppose a gene g (of length k) does not have any exons. How many different types of protein can be produced from g?
      1. 0
      2. 1
      3. 5\(^{k}\)
      4. 4\(^{k}\)
      5. None of these

      A published solution is not available for this question yet.

      Question 8 NAT · 3.0 marks

      You fly to an alien world and are surprised to find life that follows the same central dogma principle. The difference is that the alien life has 5 different nucleotides. Answer the given subquestions with respect to the same.
      Suppose this alien life has 600 distinct amino acids that make up protein sequences. What is your best guess on the length of each codon in this alien species?

        A published solution is not available for this question yet.

        Question 9 NAT · 3.0 marks

        You fly to an alien world and are surprised to find life that follows the same central dogma principle. The difference is that the alien life has 5 different nucleotides. Answer the given subquestions with respect to the same.
        Suppose this planet cannot block out harmful radiation from space, making this alien life prone to acquiring a very high number of DNA mutations. Then, what is your best guess for the minimum length of each codon?

          A published solution is not available for this question yet.

          Question 10 NAT · 4.0 marks

          Consider the following k-mers found from the genome sequence of some organism. ATG,CAT, TAG,GAT,TTA,AAT, ATA, AGA, ATC, TGC,GCA Answer the given subquestions with respect to the corresponding overlap graph.
          How many nodes are there in the graph?

            A published solution is not available for this question yet.

            Question 11 NAT · 5.0 marks

            Consider the following k-mers found from the genome sequence of some organism. ATG,CAT, TAG,GAT,TTA,AAT, ATA, AGA, ATC, TGC,GCA Answer the given subquestions with respect to the corresponding overlap graph.
            How many edges are there in the graph?

              A published solution is not available for this question yet.

              Question 12 NAT · 5.0 marks

              Consider the alignment graph based DP table below to find the best global alignment between two strings (represented along the rows and the columns). The DP table has (n + 1) x (m + 1) entries i.e., DP [0, 0] to DP [n,m], where n is length of first string and m is length of second string. DP [i, j] is the score of best global alignment between the length-i prefix of the first string and length-j prefix of the second string. Fill the DP table given below and answer the given subquestions accordingly. Scoring is done as follows: [[IMAGE:ece6cb607d1eeb32_9_4]] • 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
              How many entries in the grid consists of the number 2?
              Source diagram or notation

                A published solution is not available for this question yet.

                Question 13 MCQ · 4.0 marks

                Consider the alignment graph based DP table below to find the best global alignment between two strings (represented along the rows and the columns). The DP table has (n + 1) x (m + 1) entries i.e., DP [0, 0] to DP [n,m], where n is length of first string and m is length of second string. DP [i, j] is the score of best global alignment between the length-i prefix of the first string and length-j prefix of the second string. Fill the DP table given below and answer the given subquestions accordingly. Scoring is done as follows: [[IMAGE:ece6cb607d1eeb32_9_4]] • 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
                In the global alignment, what happens to the last character of the first string? Assume the first string (top string in the alignment) is along the rows i.e., GACAT.
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                1. The last character is matched to the corresponding character in the second string.
                2. The last character is involved in a mismatch operation.
                3. The last character is inserted.
                4. The last character is deleted.

                A published solution is not available for this question yet.

                Question 14 MCQ · 2.0 marks

                Given below in Figure 2 is the BLOSUM50 scoring matrix for amino acids. Use the same as the scoring matrix and answer the given subquestions. [[IMAGE:ece6cb607d1eeb32_11_5]]
                Global alignment among which of the following pairs of the peptides results in the maximum alignment score? Here X\(^{n}\) represents the string with the amino acid X repeated n times.
                Source diagram or notation
                1. W\(^{50}\) and W\(^{50}\)
                2. RW\(^{25}\)RW\(^{25}\) and RW\(^{25}\)RW\(^{25}\)
                3. RW\(^{48}\)R and RW\(^{48}\)R
                4. R\(^{50}\) and R\(^{50}\)

                A published solution is not available for this question yet.

                Question 15 NAT · 5.0 marks

                Given below in Figure 2 is the BLOSUM50 scoring matrix for amino acids. Use the same as the scoring matrix and answer the given subquestions. [[IMAGE:ece6cb607d1eeb32_11_5]]
                The peptide STW is aligned with the peptide generated from the RNA string AGUAUGCCUCAAACUUGG. If gap opening penalty is -20 and gap extension penalty is -2, then use the genetic code given below in Figure 3 to compute the optimal global alignment score between the peptides. [[IMAGE:ece6cb607d1eeb32_12_6]]
                Source diagram or notationSource diagram or notation

                  A published solution is not available for this question yet.

                  Question 16 NAT · 2.0 marks

                  Given below in Figure 2 is the BLOSUM50 scoring matrix for amino acids. Use the same as the scoring matrix and answer the given subquestions. [[IMAGE:ece6cb607d1eeb32_11_5]]
                  Calculate the local alignment score between the same two peptides as in the previous question.
                  Source diagram or notation

                    A published solution is not available for this question yet.