R-scape (original) (raw)

R-scape looks for evidence of a conserved RNA 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). R-scape uses a null hypothesis that takes phylogenetic correlations and base composition biases into account, which can be sources of apparent pairwise covariation that are not due to conserved RNA structure.

The input is an RNA multiple sequence alignment inStockholm format, optionally (usually) with an annotated consensus 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 (or threshold for the number of false positives expected). For each covarying pair, the output also reports the inferred number of substitutions that occurred at these two positions in the phylogenetic tree, and the estimated statistical power for R-scape to detect a significantly covarying base pair when that much variation is present.

R-scape has two different modes of operation which determine how it calculates E-values. One mode analyses all possible pairs equally. The other mode requires a given consensus structure and performs two independent covariation tests: one on the set of proposed base pairs, the other on all other possible pairs. For either mode, R-scape can calculate a structure based on the observed covariations using the CaCoFold algorithm.

To see an example, you can download the Rfam seed alignment for the purine riboswitch (RF00167) - or any other Rfam RNA alignment - and upload that file to R-scape.