FoldARE - overview

FoldARE is a computatonal tool for the prediction and analysis of RNA secondary structure.

The Analysis part is composed of three different modules:

  (i) - compare pair: pairwise compares 2D structural ensembles, returning stats and graphs

  (ii) - compare m6A: creates and compares m6A vs 2D structural ensembles, returning stats and graphs (

  (iii) - compare all: multiple comparisons of 2D structural ensembles, returning stats and graphs

The compare all module

The "compare all" module runs in parallel different methods for 2D RNA structural predictions. These well established methods are: for ViennaRNA/RNAsubopt (V), RNAstructure/Fold (R), LinearFold (L), EternaFold (E).

These methods are run as ensemblers, i.e. to create structural ensembles (ordered by energetic favour) of N size (with N being determined by the "--ens_n:" parameter, default value = 20, meaning that top 20 models within the ensemble are considered)

The ensembles are then analyzed (across all methods, N top models for each):

  (i) for average frequencies of ssRNA (single stranded RNA) per position (higher value, more ssRNA content) (html output)

  (ii) for average Entropy (Shannon) per position (html output)

  (iii) for average Consensus score (how consistent is the prediction, at each position) (html output)

  (iv) for pairwise similarity for all models. The output (csv) reports aggregate scoring for each model, sorted high (top of the list=best) to low

At the top of the results page a link to Download locally all generated output files (as zip) is available.

Note: The FoldARE compare apps take in input a sequence in fasta format, limited in size (see Home page); for unlimited input size, and for further customization options, we refer to the standalone toolkit

The FoldARE toolkit is described in detail in this manuscript doi:10.64898/2026.03.04.709501

FoldARE is available as a standalone, customizable tool in github/FoldARE.