RNA locally optimal secondary structures
To understand the functional role of an RNA in the cell, it is useful to know its structure or at least an approximation of its structure such as the secondary structure. In this perspective, the energy landscape gives a useful insight into all potential conformations of the molecule. Regliss proposes to study the energy landscape of a given RNA sequence by considering all locally optimal structures. Locally optimal structures, also called saturated structures, are thermodynamically stable structures maximal for inclusion: they cannot be extended without producing a conflict between base pairs.
Visualization
For each computed structure, Regliss produces CT files and bracket files. One can get a 2D representation of the secondary structure using Naview, which is a freely-distributed program that produces plots of RNA secondary structures.
It is also possible to vizualise the set of all locally optimal secondary structures on the energy landscape graph.
Availability
You can use Regliss via the web interface.
Reference
RNA Locally Optimal Secondary Structures
A. Saffarian, M. Giraud, A. de Monte, H. Touzet
Journal of Computational Biology, 19 (10) pp 1120-1133, 2012