Consensus Structure Prediction

Sequence co-variations are a direct consequence of RNA base pairing rules and can be deduced to alignments. RNA helices normally contain only 6 out of the 16 possible combinations: the Watson-Crick pairs GC, CG, AU, UA, and the somewhat weaker wobble pairs GU and UG. Mutations in helical regions therefore have to be correlated. In particular we often find ``compensatory mutations'' where a mutation on one side of the helix is compensated by a second mutation on the other side, e.g. a C$\cdot$G pair changes into a U$\cdot$A pair. Mutations where only one pairing partner changes (such as C$\cdot$G to U$\cdot$G) are termed ``consistent mutations''.