RNAshapes

RNA shape abstraction is a unique feature that maps structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features, but disregarding helix lengths. This abstraction seamlessly integrates with dynamic programming algorithms, making it possible to utilize it during structure prediction instead of as a post-processing step. This approach significantly reduces computational overhead and can still provide a non-heuristic and complete account of properties of the molecule's folding space.

RNAshapes is a powerful software that offers three RNA analysis tools in a single package. First, it can compute a small set of representative structures of different shapes that are complete in a well-defined sense. Second, it can compute accumulated shape probabilities. Finally, the software offers comparative prediction of consensus structures as an alternative to the Sankoff Algorithm that is far more computationally expensive.

RNAshapes is available as C source code and compiled binaries that can be used on Mac OS X, Unix, and Microsoft Windows-based machines. Overall, RNAshapes is an essential software tool for any biologist, bioinformatician or computational biologist working with RNA structures, thanks to its powerful analysis tools and RNA shape abstraction feature.