A1.3

Question 1 Single best answer Level 1 1 point

In a pairwise alignment, one column holds a letter in one sequence and a dash in the other. In the vocabulary used for alignment columns, what is this column called?

  1. A gap
  2. A deletion
  3. A mismatch
  4. A substitution

Question 2 Single best answer Level 2 1 point

How do similarity and homology differ for a pair of sequences?

  1. Homology is read directly from the letters, while similarity is inferred from shared ancestry.
  2. Similarity is read directly from the letters, and high similarity proves the sequences are homologous.
  3. Similarity is read directly from the letters, while homology is inferred from shared ancestry.
  4. Similarity and homology are the same property, one given as a count and one as a percentage.

Question 3 Single best answer Level 2 1 point

A single insertion near the start of a sequence makes two closely related sequences look very different when compared position by position. Why does one insertion have such a large effect?

  1. The insertion changes the identity of every later letter, so most later positions now hold different bases.
  2. The insertion lowers similarity only at the point where it happens, adding a cluster of mismatches there.
  3. The insertion shifts every later letter by one position, so a position-by-position comparison pairs letters that were never partners.
  4. The insertion can be found only with a substitution matrix, which a position-by-position comparison does not use.

Question 4 Single best answer Level 2 1 point

On a dot plot of two sequences, a diagonal run of dots stops and then resumes one column to the side. What does this break-and-shift pattern indicate?

  1. A chance match, shown by a lone dot with no diagonal neighbors.
  2. An insertion or deletion, shown by the diagonal breaking and resuming one column over.
  3. An inversion, shown by a segment running in the opposite diagonal direction.
  4. A repeated motif, shown by a second diagonal running parallel to the main one.

Question 5 Single best answer Level 2 1 point

On a DNA dot plot, a sliding window with an identity threshold removes most lone dots while keeping true diagonals. Why does this filter work?

  1. Lone dots are dropped because they fall away from the main diagonal, which is the only region the window inspects.
  2. A lone match is common by chance, but a run of matches is rare, so a window that demands many matches keeps diagonals and drops lone dots.
  3. A single DNA match is almost never due to chance, so any lone dot the window removes must have been a plotting error rather than real.
  4. The window rescales the plot so that only the single longest diagonal remains visible, regardless of how many matches it contains.

Question 6 Single best answer Level 3 1 point

Score alignments with match \(+1\), mismatch \(-1\), and gap \(-2\), reading each column from top to bottom. Alignment 1 places GATTACA over GACTA-A. Alignment 2 places GA-TTACA over GACT-A-A. Which alignment scores higher, and what is that score?

  1. Alignment 1; score \(2\)
  2. Alignment 1; score \(3\)
  3. Alignment 2; score \(-1\)
  4. Alignment 2; score \(5\)
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