Comparative analysis for RNA secondary structures

Carnac is a software tool for analysing the secondary structure of a family of homologous RNA sequences. It aims at predicting if the sequences actually share a common secondary structure. When this structure exists, Carnac is then able to correctly recover a large amount of the folded stems. The input is a set of single-stranded RNA sequences that need not to be aligned. The folding strategy relies on a thermodynamic model with energy minimization. It combines information coming from locally conserved elements of the primary structure and mutual information between sequences with covariations too.


Carnac produces CT files. One can get a 2D representation of the secondary structure using one of the two viewers:


Web interface: click here.

Download: carnac.tar.gz. Carnac is implemented in C and freely distributed under the CECILL license. Please see the enclosed README file for installation and running instructions. A Windows executable is available in this zip archive .


If you make use of this software, please cite the following articles.

CARNAC: folding families of related RNAs
Touzet H. and Perriquet O. Nucleic Acids Research 142, 2004

Finding the common structure shared by two homologous RNAs
Perriquet O, Touzet H, Dauchet M. Bioinformatics 19(1):108-16, 2003