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##

Interpreting Scores

The resulting measure of similarity after a matching is a sum of
Dayhoff entries, and hence it is 10 times the logarithm of this
probability.
For example, a matching between two amino acid sequences with a
similiarity (or cost or score) of 238.8
means that the probability of both sequences coming from a
common ancestor, as opposed to being a random alignment, is
10^{23.88} times more likely.
Although crude, this gives a rule of thumb for estimating the
quality of a matching.

This fact makes aligning with Dayhoff matrices a soundly based
algorithm. This has been noted by many people including
[2,9,12,13] yet such
methodologies have been largely ignored.

*Gaston Gonnet*

*1998-09-15*