In the analysis of RNA and especially when regarding the secondary structure it is often required to take also suboptimal structures into account. As the number of suboptimal structures is very large and even the number of near-optimal structures grows rapidly with sequence length, these kind of analyses are quite expensive. One property of suboptimal structures is that they often only differ in a few base pairs, while maintaining the same overall shape. These are less interesting because in most cases one is interested in those structures that are rather dissimilar, meaning those having a different shape. RNAshapes is an approach to the direct folding of only those structures having a different shape.



Fri Dec 19 10:54:56 CET 2014