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Affine gaps<br />
• Penalties:<br />
g o<br />
- gap opening (e.g. -8)<br />
g e<br />
- gap extension (e.g. -2)<br />
M[i-1, j-1]<br />
X 1<br />
… X i<br />
Y 1<br />
… Y j<br />
M[i, j] =<br />
score(X[i], Y[j]) +<br />
max<br />
I x<br />
[i-1, j-1]<br />
I y<br />
[i-1, j-1]<br />
X 1<br />
… -<br />
M[i, j-1] + g<br />
I x<br />
[i, j] =<br />
o<br />
Y<br />
max<br />
1<br />
… Y j<br />
I x<br />
[i, j-1] + g e<br />
X 1<br />
…X i<br />
-<br />
Y 1<br />
…Y j-1<br />
Y j<br />
X 1<br />
… - -<br />
Y 1<br />
…Y j-1<br />
Y j<br />
I y<br />
[i, j] =<br />
max<br />
M[i-1, j] + g o<br />
I y<br />
[i-1, j] + g x<br />
• @ home: think of boundary values M[*,0], I[*,0] etc.