FoldARE-compare

FoldARE - overview

FoldARE is a computational 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 m6A module

Compare m6A module workflow diagram — Figure 1: Compare m6A module workflow - m6A variants are generated from input sequence and modifications file, then ensembles are compared between unmodified and modified sequences using ViennaRNA and RNAstructure

The "compare m6A" module takes in input TWO files: 1) an input sequence (fasta format), and 2) a text file with position to modify (as m6A): this co-input text file has to simply contain positions (numbered 1 to n, where n it the length of the input sequence), corresponding to A positions that are to be modified to m6A (the module runs a check, if the position does not correspond to an A, it is skipped).

The first step is the creation of m6A variants of the input fasta: which will work as input for the "m6A-aware" predictions. With the unmodified sequence and the m6A modified variant, compare_m6A runs in parallel two methods: ViennaRNA (V) and RNAstructure (R), currently the only available choices for this type of predictions.

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, comparing "unmodified vs m6A" for RNAstructure, for ViennaRNA, and for R&V cross comparisons:

  (i) for average frequencies of ssRNA (single strand RNA) per position (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)

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.