. Explain what Bayes’ Theorem is. Why is it controversial?
2. What is Independent Probability? Give an example using dice.
3. What is Dependent Probability? Give an example using dice.
4. What is the probability of finding the sequence “AAAAAAAAAA” in a random stretch of DNA? Show all the work.
5. Use the Sum-of-Pairs method with standard scoring (+5 Match, -4 Mismatch -16 to Open a gap, -4 to extend a gap) to compute the score for the following alignment:
AATAAAAGAGC
AATAA-ACAGC
AA-TACAGAGC
6. Create a kmer table showing all unique 3-mers and their positions(s) for the sequence AATCAGACCTATAGCAAT
7. What is a Markov chain? Provide an example, including a graph. Do not include any code
8. What is the difference between a Markov chain and an HMM? Provide an example of each. Do not include any code