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 pair module
The "compare pair" module runs in parallel two different methods for 2D RNA structural predictions. The user can select among these established methods: for ViennaRNA/RNAsubopt (V), RNAstructure/Fold (R), LinearFold (L), EternaFold (E). [default selection: E and L]
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 the 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 (html) is a heatmap, with color coding and detailed previews
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:10.64898/2026.03.04.709501FoldARE is available as a standalone, customizable tool in github/FoldARE.