RNA structure prediction.

The prediction of RNA structure can be a first important step for the functional characterization of novel ncRNAs. Especially for the very meaningful secondary structure, there is a multitude of computational prediction tools. They differ not only in algorithmic details and the underlying models but also in what exactly they are trying to predict. This chapter gives an overview of different programs that aim to predict RNA secondary structure. We will introduce the ViennaRNA software package and web server as a solution that implements most of the varieties of RNA secondary structure prediction that have been published over the years. We focus on algorithms going beyond the mere prediction of a static structure.