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Global alignment

Alignment that is carried out from beginning of the sequence to the end of the sequence in order to find the optimal alignment

step

a) Fill first row and first column with 0.

b)The gap score is added to the previous column or row

Example

Row 2 Row 3

0+(-2)= -2 -2+(-2)=-4

STEP 1: Fill up the matrix using recurrence relation.

1) Start from the upper left find the maximum score Diagonal value

Match: add match score

A- A -2+1=-1

Mismatch: add the mismatch score

G-A -2+(-1)= -3

Left and right: Add the gap score

A-C -6+(-2)=-8

STEP 2:Matrix fill up.

2)Find the maximum value and mark the arrow where the value come from.

STEP 2: Matrix fill up.

Traceback to obtained maximum value from the obtained data we could see that the bottom right-hand value is -1where the maximum value is 0 which located at the diagonal left. Hence reach to the 0 through traceback With this the optimum alignment could be found