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PART V. USING THE DYNAMIC PROGRAMMING METHOD TO CALCULATE THE LOCAL ALIGNMENT OF TWO SHORT SEQUENCES BY HAND
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.
 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.)
 Use the BLOSUM62 matrix and BLASTP gap penalties of –11,–1. What is the optimal alignment and score between these two sequences?


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