Fallmann, J.,Will, S.,Engelhardt, J.,Gruning, B. A.,Backofen, R.,Stadler, P. F.

In the realm of nucleic acid structures, secondary structure forms a conceptually important intermediate level of description and explains the dominating part of the free energy of structure formation. Secondary structures are well conserved over evolutionary time-scales and for many classes of RNAs evolve slower than the underlying primary sequences. Given the close link between structure and function, secondary structure is routinely used as a basis to explain experimental findings. Recent technological advances, finally, have made it possible to assay secondary structure directly using high throughput methods. From a computational biology point of view, secondary structures have a special role because they can be computed efficiently using exact dynamic programming algorithms. In this contribution we provide a short overview of RNA folding algorithms, recent additions and variations and address methods to align, compare, and cluster RNA structures, followed by a tabular summary of the most important software suites in the fields.