1

2

3

4

5

A

G

T

C

A

1

C

0

0

0

1

0

2

A

1

0

0

0

1

3

G

0

1

0

0

0

4

G

0

3

2

1

0

5

C

1

1

1

2

0

6

A

1

0

0

0

1

7.9 shows the final result of the forward propagation for aligning

sequences using the Needleman-Wunsch algorithm.

ൌݏସ,ଶ൅max൛ܯହ,ଷ, ܯ଺,ସܯହ,ሺଷ,ସ,ହሻൟൌ1 ൅max ሼ1, 0, 2ሽൌ3

e 7.9. The forward propagation result for aligning CAGGCA with AGTCA.

1

2

3

4

5

A

G

T

C

A

1

C

3

2

2

2

0

2

A

4

2

2

1

1

3

G

3

3

2

1

0

4

G

2

3

2

1

0

5

C

1

1

1

2

0

6

A

1

0

0

0

1

he backward propagation stage

ward propagation stage of the Needleman-Wunsch algorithm is

ind the best alignment between two sequences. The procedure

m the top-left corner cell and ends at the bottom-right corner cell.

is that every residue in rows or in columns cannot be visited more

e. Besides, whenever a residue is passed over, a gap is inserted.

the cell (2, 1) had the highest score four in the whole table. For

the alignment is shown below, where the first residue C of

x was aligned with a gap while the second residue A of sequence

gned with the first residue A of sequence y.