Please enter below any questions you have about material that is still unclear after today's class. If you have no questions, please just enter "no questions". Putting 'no questions', means you will be able to answer the following questions,
1. What is the goal of motif search?
2. Why will finding most_frequent_k-mrs perform a poor job if you use it to search motif in a set of strings?
3. Let's say, you have t strings and each of them have length n. You are, now given t k-mers of length k, one from each of the t strings. You are also told that these k-mers represents the potential motif binding sites in those strings. How would you measure that goodness of those k-mers which indicates that those t k-mers represent potential motif binding profile.
4. What is entropy?
5. For a set of motifs, is entropy more biologically meaningful than count and profile matrix as a scoring function? Why?