Lecture2

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Unformatted text preview: Visualized and represent indels in v and w with score 0. represent matches with score 1. The score of the alignment path is 5. Dynamic Programming Visualized Every path in the edit graph corresponds to an alignment: Define Rules •  Score for match: +1 •  Score for mismatch: 0 •  Score for gap: 0 Let si,j be the total score at posi1on i, j then we have that it is equal to the maximum of {si ­1, j ­1 + 1 (if vi = wj), si ­1, j (otherwise: gap or mismatch)} Dynamic Programming Example Ini1alize 1st row and 1st column to be all zeroes. Or, to be more precise, ini1alize 0th row and 0th column to be all zeroes. Dynamic Programming Example Si,j = maximum of : Si-1, j-1 Si-1, j Si, j-1 value from NW +1, if vi = wj value from North (top) value from West (left) Alignment: Backtracking Arrows show where the score originated. •  if from the top •  if from the leZ •  if vi = wj Backtracking Example Find a match in row and column 2. i=2, j=2,5 is a m...
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This note was uploaded on 02/10/2014 for the course CS 680 taught by Professor Staff during the Fall '08 term at Colorado State.

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