 Solution

Dynamic programming stores answers to overlapping subproblems so they can be reused. Its optimal substructure requirement, the principle of optimality, says that an optimal answer's remaining subproblem solution must itself be optimal once the final decision and state are fixed.

For global sequence alignment without mismatches, use the two prefix lengths as the state. A final column is either a letter of the first string opposite a gap, a gap opposite a letter of the second, or two equal letters. Removing that column leaves one of three smaller prefix problems. If its alignment were suboptimal, replacing it by a better alignment would improve the whole answer. Many different alignments reach the same prefix state, making reuse valuable. Unequal-letter columns and double-gap columns are forbidden, rather than assigned ordinary finite penalties.