Methods for Predicting RNA Secondary Structure

Authors: Kornelia Aigner Fabian Dreßen Gerhard Steger

Publish Date: 2012

Volume: , Issue: , Pages: 19-41

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Abstract

The formation of RNA structure is a hierarchical process the secondary structure builds up by thermodynamically favorable stacks of base pairs helix formation and unfavorable loops nonWatson–Crick base pairs hairpin internal and bulge loops junctions The tertiary structure folds on top of the thermodynamically optimal or closetooptimal secondary structure by formation of pseudoknots base triples and/or stacking of helices In this chapter we will concentrate on available algorithms and tools for calculating RNA secondary structures as the basis for further prediction or experimental determination of higher order structures We give an introduction to the thermodynamic RNA folding model and an overview of methods to predict thermodynamically optimal and suboptimal secondary structures with and without pseudoknots for a single RNA Furthermore we summarize methods that predict a common or consensus structure for a set of homologous RNAs such methods take advantage of the fact that the structures of noncoding RNAs are more conserved and more critical for their biological function than their sequences

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