Alignment consistency. A violation of RNA structural alignment consistency is shown (left), together with a possible correction (right) – see text for details. Note that the inconsistent alignment may maximise sequence similarity, showing 3 mismatches versus 1 mismatch and 2 indels, with the concrete outcome depending on the gap scoring used. Inconsistency is the reason why it is dangerous to align two structures in string representation by a standard sequence alignment algorithm. Inconsistency is hard to detect by human eye inspection, and structural alignments in databases are not always free from consistency violations.
Gardner and Giegerich BMC Bioinformatics 2004 5:140 doi:10.1186/1471-2105-5-140