A1.4

Question 1 Single best answer Level 2 1 point

Why can dynamic programming find the best alignment without listing and scoring every possible alignment?

  1. It samples a large random set of alignments and keeps the best, which is almost always the true optimum.
  2. It still scores every alignment, but runs faster by reusing one substitution-matrix lookup table across them.
  3. It discards any alignment that contains a gap early on, cutting most possibilities before it scores them.
  4. Each prefix pair’s best sub-alignment is built from shorter ones, so each pair is solved once and reused.

Question 2 Single best answer Level 3 1 point

Fill a Needleman-Wunsch matrix for the top sequence GATC and the side sequence GTC, using match \(+1\), mismatch \(-1\), and gap \(-2\). What is the optimal global alignment score?

  1. \(-1\)
  2. \(3\)
  3. \(-3\)
  4. \(1\)

Question 3 Single best answer Level 2 1 point

How do global and local alignment differ in what they report?

  1. Global alignment permits gaps, while local alignment forbids them and allows only exact matches.
  2. Global alignment uses one gap penalty, while local alignment uses another, but both align end to end.
  3. Global alignment reports only the best-matching region, while local alignment lines up the full lengths.
  4. Global alignment scores the sequences end to end, while local alignment reports only the highest-scoring shared region.

Question 4 Single best answer Level 3 1 point

Run Smith-Waterman on the top sequence AGCT and the side sequence GC, using match \(+1\), mismatch \(-1\), gap \(-2\), and a floor of \(0\). What is the optimal local alignment score? (You can do this without filling out a matrix; look for similarities between sequences.)

  1. \(-2\)
  2. \(0\)
  3. \(2\)
  4. \(1\)

Question 5 Single best answer Level 2 1 point

In BLOSUM62 the leucine-isoleucine pair scores \(+2\), while the leucine-aspartate pair scores \(-4\). What does the sign of a substitution-matrix entry tell you?

  1. The sign reflects how frequent each amino acid is on its own, not how often the two are swapped for each other.
  2. A positive score means the swap is disfavored and rare, while a negative score means it is favored and common.
  3. A positive score means the swap is seen more often than chance and tolerated; a negative score, less often and penalized.
  4. A positive score means the two residues are chemically identical, and a negative score means they are in different classes.

Question 6 Single best answer Level 2 1 point

How does a linear gap penalty differ from an affine gap penalty?

  1. A linear penalty charges the same for every gap position, while affine charges a large open cost plus a smaller extend cost per extra position.
  2. Both charge the gap length times a per-position amount, but an affine penalty makes that amount positive so gaps raise the score.
  3. A linear penalty is used for DNA while an affine penalty is used for protein, though the two share the same formula.
  4. A linear penalty charges per position, while an affine penalty charges a single flat fee for the whole gap regardless of its length.

Question 7 Single best answer Level 3 1 point

An optimal global alignment currently uses two gaps and no mismatches under match \(+1\), mismatch \(-1\), and gap \(-1\). If the gap becomes more costly, changing from \(-1\) to \(-3\) per position, how will the new optimal alignment most likely change?

  1. It will use more gaps to avoid the mismatches, which are now the costlier option.
  2. It will keep the same gaps, and the higher penalty will push the total score up.
  3. It will not change, because the match and mismatch scores are the same as before.
  4. It will use fewer gaps and take more mismatches, since a gap now costs more than a mismatch.

Question 8 Single best answer Level 4 1 point

A 30-residue query is compared against a 5,000-residue genome region. You expect the query to match one internal stretch of the long sequence, and you expect any indels to occur as single multi-residue events. Which combination of alignment method and gap penalty best fits this pair?

  1. Global alignment with a linear gap penalty.
  2. Global alignment with an affine gap penalty.
  3. Local alignment with an affine gap penalty.
  4. Local alignment with a linear gap penalty.
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