The program will take two sequences to be aligned as input. You may use a simple scoring scheme. A user should be allowed to enter the parameter for the match, mismatch, and gap respectively. The output is the optimal alignment score and the optimal alignment. you are also encouraged to use PAM250 matrix to the alignment of two protein sequences,
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I've briefly read through the algorithm description, looks not too hard to implement. I will need to ask you some questions about the requirements and the internals of the algorithm.