We present a method for attributing a measure of reliability to a resi
due pair in an optimal alignment of two protein sequences. Validation
based on a database of structurally correct alignments [Pascarella and
Argos (1992) Protein Engng, 5, 121-137] shows that correctly aligned
parts of a sequence alignment systematically receive high scores in th
is measure, The higher the sequence similarity between two sequences,
the larger is the fraction found of the correct parts of the alignment
, We used these observations to design a program that draws a reliabil
ity curve along an optimal alignment reflecting the chances for each r
esidue pair to be aligned correctly.