We are here intererested in finding an optimal alignment between a part of x and a part of y.
The notion of distance is not suitable anymore to get the result thus we have to use the notion of similarity.
We use the following recurrence formula ():
where substitutions, deletions and insertions are given negative values.
To find an optimal local alignment, it is sufficient to find the largest value in the table T and to trace back the path from the square containing this value.
x = YHCQPGK, y = LAHYQQKPGKA, Sub(a,a) = 1, Sub(a,b) = -3, Del(a) = Ins(a) = -1.
PGK corresponds to the highest area of similarity between YWCQPGK and LAWYQQKPGKA.