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Recent advances in RNA folding
- Fallmann, Jörg, Will, Sebastian, Engelhardt, Jan, Grüning, Björn, Backofen, Rolf, Stadler, Peter F.
- Journal of biotechnology 2017
- Gibbs free energy, RNA, RNA folding, algorithms, bioinformatics, computer software, dynamic programming
- 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.