Introduction to RNA secondary structure comparison

Many methods have been proposed for RNA secondary structure comparison, and new ones are still being developed. In this chapter, we first consider structure representations and discuss their suitability for structure comparison. Then, we take a look at the more commonly used methods, restricting ourselves to structures without pseudo-knots. For comparing structures of the same sequence, we study base pair distances. For structures of different sequences (and of different length), we study variants of the tree edit model. We name some of the available tools and give pointers to the literature. We end with a short review on comparing structures with pseudo-knots as an unsolved problem and topic of active research.