RNA energy landscape and locally optimal secondary structures
Regliss proposes to study the energy landscape of a given RNA sequence by considering all locally optimal seondary structures. Locally optimal 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.