A
A
C
U
C
C
A
A
C
U
C
C
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
1
1
D
D
D
0
1
1
0
0.67
0
0.33
D
D
D
D
0
0
0.67
0.67
1
0.67
0.33
D
D
D
H
H
0
0
0
0.33
1.67
1.33
1
D
D
H
H
0
0
0
0
0
1.33
1
D
D
0
1
1
0
0
1
1
D
D
V
D
he backward propagation stage
th-Waterman algorithm does not necessarily start from the
ght corner when searching for the best alignment in the backward
on stage. Instead, it starts from a cell with the maximum
t score and move towards the top-left corner cell. The
on stops at a cell with a zero alignment score.
Table 7.16. The backward propagation result.
0
2
3
4
2
3
4
A
C
U
A
C
U
3
A
0
1
0
1
D
D
4
U
0
0
0.67
1
D
D
5
U
0
0
0
1.67
D
hese two sequences, the maximum alignment score was 1.67 in
5, 4). The backward propagation search thus started from this cell,
all the remaining residues from two sequences, i.e., GA from
x and CC from sequence y. The alignment score of this cell was
f a diagonal move from the cell (4, 3). The alignment score of the
) was also a result of a diagonal move from the cell (3, 2). The
t score of cell (3, 2) was again a result of a diagonal move from
2, 1). However, the alignment score of the cell (2, 1) was zero.
ch of the best local alignment thus stopped here. The previous
GC of sequence x and the previous residue A of sequence y were
red. The maximum alignment score was 1.67 in the cell (5, 4)
n Table 7.16. The final alignment using the Smith-Waterman