Example test questions

  1. True or false. Given the mRNA sequence of a protein-coding gene, the corresponding amino acid sequence can be unambiguously determined.
  1. True of false. Given the amino acid sequence of a protein, the corresponding gene (DNA sequence) can be unambiguously determined.
  1. The reverse complementary sequence of DNA sequence CACGTCAGCTC is ______.
  1. The asymptotic running time of the Smith-Waterman algorithm (local alignment) is ___ that of the Needleman-Wunsch Algorithm.
  2. Equal to
  3. Larger than
  4. Smaller than
  1. In local alignment, which scoring matrix is better for aligning sequences from closely related species?
  2. Match = 1, Mismatch = -3;
  3. Match = 3, Mismatch = -1;
  1. True or false. When aligning two DNA sequences of 100bp each, an alignment score of 95 or above is sufficient to claim that the two sequences are evolutionarily related.
  1. Given the following PWM of a transcription factor binding motif, the consequence sequence is ______

A / 0.04 / 0.55 / 0.01 / 0.60 / 0.05 / 0.10
C / 0.05 / 0.15 / 0.01 / 0.20 / 0.05 / 0.80
G / 0.01 / 0.25 / 0.18 / 0.10 / 0.60 / 0.05
T / 0.90 / 0.15 / 0.80 / 0.10 / 0.30 / 0.05
  1. Which of the following image is the correct sequence logo for the PWM?

Image 1, image 2, image 3

  1. True or false. Suffix array is invented to speed up the construction of suffix tree but it uses more memory than suffix tree.
  1. Jack went to see his doctor and his doctor asked him to screen for some type of disease. The results turned out to be positive. It is known that the screening technology is accurate: for those with the disease, the screening will report positive 99.99% of the time, and for those without the disease, the screening will report negative 99.99% of the time. It is also known that the disease occurs in one out of 1 million people in general but certain popular may have higher risk. Which of the following statements are true?
  1. We are 99.99% sure that Jack has the disease.
  2. Without further evidence, the probability that Jack has the disease is still very small (less than 1%).
  3. Jack feels very healthy and shouldn’t worry about it.
  4. Jack should talk to his doctor and found out more information about what are the other risk factors.
  5. Jack should ask his doctor why his doctor suggested him to do the screening and what are the other symptoms of the diseases.
  1. The boxplot below shows the expression levels of all genes in 10 patients (5 good outcomes and 5 bad outcomes).

True or false. As shown in the figure, patients with poor outcomes are more likely to have higher gene expression levels. The next step is probably to compare the two sets of data and identify which genes have higher expression levels in poor outcomes than good outcomes.