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The algorithm<br />
Goal: find the maximal scoring alignment<br />
Scores: m match, -s mismatch, -g for<br />
insertion/deletion<br />
The best alignment for X[1…i]<br />
is called M[i, j]<br />
3 ways to extend the alignment<br />
and Y[1…j]<br />
X[1…i-1]<br />
Y[1…j-1] X[i] X[1…i] -<br />
Y[j] Y[1…j-1]Y[j]<br />
X[1…i-1] X[i]<br />
Y[1…j] -<br />
M[i,j] =<br />
M[i-1, j-1]<br />
+ m<br />
- s<br />
M[i, j-1] - g<br />
M[i-1, j] - g
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