20 points
Assigned Tuesday, February 3
Due Tuesday, February 10 by 11:59pm
In this mini-homework, you are to perform optimal pairwise global alignments using the dynamic programming algorithm discussed in class. Choose a PAM or BLOSUM scoring matrix from the web as the basis of the alignment, explain and justify your choice of matrix, and provide a link to the matrix from within your wiki. Also, choose a gap penalty and justify it. Then, apply the dynamic programming algorithm to pairwise align the same pairs of sequences you did in mini-homework 0.5 (i.e., the four parent-child pairs). Finally, briefly compare and contrast the four alignments you generated with dynamic programming to those you derived from the evolutionary process of mini-homework 0.5. In particular, highlight any major differences and speculate what effect your choice of scoring matrix might have had.
Take your writeup and your alignments and add them to your sequence descriptions and alignments in your personal wiki, which is already linked in from the course wiki. Do not remove your previous results from your wiki; keep everything as a single, comprehensive document.