4. Bioinformatics prediction of RNA structure

This section alone would merit a full article, given the ever-increasing importance of and interest in RNA sequences, particularly non-coding sequences which may or may not be structured. We will therefore only mention a few introductory notions, enabling the reader to move on to more specialized literature.

Despite the differences between proteins and RNAs, the prediction procedures follow a fairly similar pattern, i.e. secondary structure prediction followed by tertiary structure prediction. In contrast to proteins, this procedure is more consistent with the hierarchical tertiary folding process of RNAs than that of proteins, which is rarely so. The secondary structure of RNA thus results from the thermodynamically favorable stacking of base pairs. This favorable stacking leads to helical structures separated by loop regions that are generally thermodynamically...