Dynamic Programming

Today you will calculate the optimal alignment of the following two sequences:

• TCGTGCACC
• TTTCGCACCG

Draw a dynamic programming matrix for the two sequences above. Then answer the following questions. Turn in both the matrix and the answers to the questions.

1. What is the maximum possible score for this alignment?
2. What scoring matrix did you use?
3. Is there a penalty for gaps at the beginning/end of the sequences?
4. Is the penalty for opening a gap the same as the penalty for extending a gap? Do you think there should be difference between these penalties? Why or why not?