The fast way Morten Nielsen BioSys, DTU. The fast algorithm (O2) Database (m) Query (n) Open a...
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The fast way Morten Nielsen BioSys, DTU
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Transcript of The fast way Morten Nielsen BioSys, DTU. The fast algorithm (O2) Database (m) Query (n) Open a...
The fast way
Morten NielsenBioSys, DTU
The fast algorithm (O2)
Database (m)
Qu
ery
(n)
Open a gap Extending a gap
P
Q
Affine gap penalties
The fast algorithm (cont.)
Database (m)
Qu
ery
(n)
P
Q
The fast algorithm (cont.)
Database (m)
Qu
ery
(n)
P
Q
eij = 1 matcheij = 2 gap-opening database eij = 3 gap-extension database eij = 4 gap-opening query eij = 5 gap-extension query
E14
5
2
3
How does it work (D,Q,P, and E-matrices)D Q
m
n
V L I L P
V
L
L
P-1
0
0
0
0
000000
V L I L P
V
L
L
P10
0
0
0
0
000000
PV L I L P
V
L
L
P-1
0
0
0
0
000000
E
V L I L P
V
L
L
P1
0
0
0
0
000000
How does it work (D,Q,P, and E-matrices)D Q
m
n
V L I L P
V
L
L
P-1 -1
0
0
0
0
000000
V L I L P
V
L
L
P5 10
0
0
0
0
000000
PV L I L P
V
L
L
P5 -1
0
0
0
0
000000
E
V L I L P
V
L
L
P4 1
0
0
0
0
000000
How does it work (D,Q,P, and E-matrices)D Q
P
m
n
E
11
V L I L P
V
L
L
P
10 12 9 3
8 4 5 10 4
2 -2 -1 0 5
0 -1 -1 -1 -1
0
0
0
0
000000
1
V L I L P
V
L
L
P
1 1 3 3
5 1 1 1 3
5 1 4 1 2
5 5 5 4 1
0
0
0
0
000000
18
V L I L P
V
L
L
P
14 9 3 0
11 12 5 -1 -1
8 9 10 0 -1
2 3 4 5 -1
0
0
0
0
000000
20
V L I L P
V
L
L
P
18 14 9 3
11 15 17 10 4
8 9 10 15 5
2 3 4 5 10
0
0
0
0
000000
