The following visualizations provide a general overview on the base pairing potential of both the wildtype (WT) and SNP-mutated (mut) RNA sequence.

The dot plot (top-left) visualizes the base pairing potential of both the wildtype and the mutant RNA in a heatmap-like fashion. That is the darker the dot, the higher is the probability that the respective sequence positions form a base pair. Probabilities derived from the Boltzmann distributed energies of all structures that can be formed by an RNA given the folding constraints (e.g. maximal base pair span). The mutated position is highlighted by red dotted lines.
The same base pair probabilities are depicted via circular plots (top-left and -right) and arc plots (bottom-left and -right). Wildtype base pairing (top-middle) refers to the upper right part of the dot plot while mutant base pairing (top-right) covers information of the lower left part. In both, higher base pairing potential is reflected in darker hues of respective gray lines. The SNP position is marked by a red line in the outer ring within the mutant's plot on the right.
Arc plot representations (bottom) of the base pairing probabilities are analogous to the circular plots but use a heatmap-like arc coloring. That is highest probabilities are dark red while low probable base pairs are depicted in yellow.
Base pairing probabilities were extracted from the following dot plots: [WT.ps] [mut.ps] (RNAplfold (Bernhart et al., 2011)).

To better see the often local structural changes induced by a SNP mutation, the differences of the mutant's base pairing potential compared to the wildtype sequence are given below. Furthermore, the effects on the single-strandedness, i.e. accessibility, are visualized in terms of single-position unpaired probabilities within the structural ensembles.

The dot plot (top-left) provides the absolute differences of the base pairing probabilities of SNP-mutated vs. wildtype RNA, i.e. in detail Pr(bp in WT) - Pr(bp in mut). The upper right part of (top-left) visualizes positive differences, i.e. a weakening of the base pairing potential, while the lower left reports (absolute values) of negative differences, i.e. base pairs with increased probability within the mutant. Again, darker hues reflect higher absolute changes. The mutated position is highlighted by red dotted lines.
In the (top-middle) and (top-right) respective visualizations are given in a circular plotting mode. Darker gray scales refer to higher absolute changes. The SNP position is annotated by a red bar in the outer ring.

Arc plot representations (top) of the absolute change of base pairing probabilities are analogous to the circular plots but use a heatmap-like arc coloring. That is highest probabilities are dark red while low probable base pairs are depicted in yellow. Weakened base pairs are shown on top while strengthened base pairs are depicted below the sequence. Mutations are highlighted by vertical dashed lines.
In case the effects are local, only the respective subsequence is shown. Full length depictions are available via respective links.

The dot plot (left) provides the differences of the base pairing probabilities of SNP-mutated vs. wildtype RNA, i.e. in detail Pr(bp in WT) - Pr(bp in mut). That is base pairs weakened by the mutation are in blue while higher base pair probability in the mutant are depicted in red. The mutated position is highlighted by red dotted lines.
The (right) accessibility profiles of both sequences and their differences provide an assessment of the mutation's effect on the RNA's single-strandedness, which is e.g. strongly related to its interaction potential with other RNAs or proteins. Accessibility is measured in terms of local single-position unpaired probabilities (RNAplfold (Bernhart et al., 2011)); extracted from the following files: [WT.txt] [mut.txt] The mutated position is highlighted by a red line.

Assessment using remuRNA

Assessment using RNAsnp mode 1

Assessment using RNAsnp mode 2

RNAsnp (Sabarinathan et al., ‎2013) focuses on the local regions of maximal structural change between mutant and wildtype RNA. The mutation effects are quantified in terms of empirical P values. To this end, the RNAsnp software uses extensive precomputed tables of the distribution of SNP effects as function of length and GC content.
(Mode 1) is designed to predict the effect of SNPs on short RNA sequences (< 1000nts), where the base pair probabilities of the wildtype and mutant RNA sequences are calculated using the global folding method RNAfold. (distance) = the difference between the base pair probabilities of wildtype and mutant computed as Euclidean base pair distance. Finally, the interval with maximum base pairing distance or minimum correlation coefficient and the corresponding p-value is reported.
(Mode 2) is designed to predict the effect of SNPs on large RNA sequence using the local folding method RNAplfold with the default parameters -W 200 and -L 120. As a first step, the structural difference is calculated using the Euclidean distance measure for all sequence intervals of fixed window length. In the second step, the sequence interval with maximum base pair distance is selected to re-compute the difference for all internal local intervals. The interval with maximum base pair distance and the corresponding p-value is reported.
RNAsnp might provide additional warnings or error messages e.g. for very short sequences, which are available below the table if reported. For further details, we refer to the Help page of RNAsnp. If you use the scores in your research, please also cite (Sabarinathan et al., ‎2013) along with the version information from below.