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Recent advances in RNA folding

: Fallmann, J.; Will, S.; Engelhardt, J.; Grüning, B.; Backofen, R.; Stadler, P.F.

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Journal of biotechnology 261 (2017), pp.97-104
ISSN: 0168-1656
ISSN: 1389-0352
ISSN: 1873-4863
Bundesministerium für Bildung und Forschung BMBF
Bundesministerium für Bildung und Forschung BMBF
Journal Article, Electronic Publication
Fraunhofer IZI ()

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.