Incongruences Between Sequence and Secondary Structure Alignments of Nucleic Acids

This is a preliminary draft of a research manuscript in preparation. It is intended only as accompanying material for the course “Advanced Methods in Bioinformatics” at Leipzig University and will soon be superseeded by a complete manuscript. Motivation: Independent selection pressures on sequence elements and secondary structure may result in incongruencies between sequence alignments and strueture alignments of the same molecules: Even though the structure are highly similar, base pairs not formed between homologous sequence positions and – conversely – structurally analogous base pairs involve non-homologous sequence positions. No single alignment is capable of faithfully representing such cases. Instead a pair of coupled alignments, one representing sequence evolution and one describing evolution of the structures must be employed.