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Local similarity

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 ([18]):

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.

Example :
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.



List of web sites Sequence comparison Cost depending on the length of the gaps
Next: List of web sites Up: Sequence comparison Previous: Cost depending

e-mails: {Christian.Charras, Thierry.Lecroq}@laposte.net
Thu Feb 19 10:23:29 WET 1998