1. Alignments II

2. Dynamic programming table

3. Maximum sum subarray problem
Given array of numbers [a_1, a_2, ... a_n] find
continuous sub array with maximum sum.

4. Local alignment
Find most common regions of two sequences

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)

7. FItting alignment
Align the whole pattern(TAGATA) against
substring of the text(GTAGGCTTAAGGTTA)

8. Affine gap penalty
total_penalty =
gap_open + gap_extend * (length-1)
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