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Predicting the likely quality of alignment

Barton and Sternberg (1987a,b) considered families of proteins for which the three dimensional structure of at least two members had been solved by x-ray crystallography. The alignment obtained by comparing the tertiary structures was used as a 'standard' against which to test the Needleman and Wunsch (1970) sequence alignment algorithm.

In summary; if the significance score obtained for the pairwise comparison of two sequences is greater than 5-6 S.D. then there is a high probability that the sequences will be correctly aligned over most of the regions that belong to core secondary structures. Whilst this observation does not mean that alignments of sequence pairs scoring less than 5.0 S.D. are meaningless, alignments in this region should be treated with caution and additional evidence in support of the particular alignment should be sought. Conversely, if two sequences score greater than 15.0 S.D. then the alignment is likely to be correct over most of its length.