An algorithm for shape rule application is presented. A shape rule a -> |3 applies to a labelled shape 7 whenever there is a transformation r that makes ot a subshape of 7. In this case, a new labelled shape can be obtained by replacing the occurrence of 7(a) in 7 with r(|3). The algorithm required for this process is developed in this paper. This algorithm determines all possible distinct tran...

Algorithms for the Boolean operations and relations on shapes and labelled shapes are presented. This paper has two parts. The first part accomplishes two objectives. First, an efficient and uniform representation for shapes is presented, which is based on a linear order on the maximal lines of a shape. Second, simple and efficient algorithms for the Boolean operations on shapes (shape union, d...

MOTIVATION Abstract shape analysis, first proposed in 2004, allows one to extract several relevant structures from the folding space of an RNA sequence, preferable to focusing in a single structure of minimal free energy. We report recent extensions to this approach. RESULTS We have rebuilt the original RNAshapes as a repository of components that allows us to integrate several established to...