A perspective on the algorithms predicting and evaluating the RNA secondary structure

Investigating the RNA structure contributes greatly to understand RNA roles in cellular processes. Indeed, functional RNAs show specific instrumental sub-structures for their interaction with other molecules. The RNA structure prediction will provide fundamental insights into developing hypothesis connecting function to structure, but it is a challenging and unsolved task yet. We aim at discussing the current status of the widespread RNA folding tools and comparing their performances on RNA families with known structure, in order to estimate how much the predictions are close to the experimental folding. A comprehensive understanding of RNA folding could highlight further roles of long non-coding RNA in the gene expression regulation and in the epigenetic regulatory pathways in physiological and pathological conditions of a living cell.