RNA Structural Covariation Above Phylogenetic Expectation
R-scape looks for evidence of a conserved RNA secondary structure by measuring pairwise covariations observed in an input multiple sequence alignment. It analyzes all possible pairs, including those in your proposed structure (if you provide one).
The input is an RNA multiple sequence alignment in Stockholm format, optionally (usually) with an annotated secondary structure. The structure may include pseudoknots. Only the first alignment in the file is analyzed; if you submit a Stockholm file containing more than one alignment, the others are ignored.
The output is a list of covarying pairs that are statistically significant at a given E-value. The E-value (expectation value) sets a threshold for the number of false positives expected. R-scape uses a null hypothesis that takes phylogenetic correlations and base composition biases into account, sources of apparent pairwise covariation that are not due to conserved RNA structure.
If the input alignment does not have an annotated secondary structure, R-scape calculates the structure with the highest amount of covariation for the target E-value (using constrained CYK folding with the probabilistic TORNADO "basic_grammar" model).
To see an example, you can download the Rfam12.0 seed alignment for the Purine Riboswitch, RF00167 or any other Rfam RNA alignment, and upload that file to R-scape.
Analyze an RNA alignment
Find potential base pairs with statistically significant covariation support.