. Explain what Bayes’ Theorem is. Why is it controversial?
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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:
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