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Evaluation of alignment quality

Sequence alignments are compared to the standard of truth obtained from structure-structure alignments, using a version of the program SSAP from Willie Taylor. The mean alignment shift error, $\overline{S}$ is calculated from all the pairs of equivalences in common between the structural and sequence alignments. $\overline{S}$ is a useful measure, but it is important to remember this is a single number summarising a whole array of alignment errors. In particular, no thresholds of sequence or structural similarity (other than using the threshold within SSAP) are used to restrict comparisons to confidently aligned regions, and thus large but unimportant alignment errors in loops connecting secondary structure may cloud the results.