RNAshape abstraction maps structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features, but disregarding helix lengths. Shape abstraction integrates well with dynamic programming algorithms, and hence it can be applied during structure prediction rather than afterwards. This avoids exponential explosion and can still give us a non-heuristic and complete account of properties of the molecule’s folding space.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install rnashapes
and update with:
conda update rnashapes
A Docker container is available at https://quay.io/repository/biocontainers/rnashapes.