The BLASTP algorithm performs a local alignment between a query sequence and a matching database sequence using the dynamic programming algorithm with the BLOSUM62 scoring matrix, a gap opening penalty of �11, and a gap extension penalty of –1 (i.e., a gap of length 1 has a penalty of �11, one of length 2, �12, etc.). Align the sequences MDPW and MEDPW using the Smith�Waterman algorithm described in the dynamic programming notes by following the global alignment example given in the notes, but using the Smith�Waterman algorithm.

1. Make a matrix for keeping track of best scores and a second matrix to keep track of the moves that give the best scores. (Hint: The alignment of M's, P's, and W's all give high scores, so the problem boils down to how to align D with ED and is actually quite a trivial problem.)
2. Use the BLOSUM62 matrix and BLASTP gap penalties of �11,�1. What is the optimal alignment and score between these two sequences?