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Bioalgo 2013-07-alignment-2
- 3. Maximum sum subarray problem
Given array of numbers [a_1, a_2, ... a_n] find
continuous sub array with maximum sum.
- 5. Formal problem
Find two substrings with maximal score
Score[0, i] = -gap_penalty * i
Score[j, 0] = -gap_penalty * j
Score[i, j] =
max(
Score[i-1, j] - gap_penalty,
Score[i, j-1] - gap_penalty,
Score[i, j] + match_score)
- 6. Smith-Waterman
Score[0, i] = 0
Score[j, 0] = 0
Score[i, j] =
max(
0,
Score[i-1, j] - gap_penalty,
Score[i, j-1] - gap_penalty,
Score[i, j] + match_score)