## 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