Predicting secondary structure for a set of homologous RNA sequences
Carnac is a software tool for analysing the hypothetical secondary structure of a family of homologous RNA. 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:
- Naview is a freely-distributed program that produces plots of RNA secondary structure
- RNAfamily is a home-made viewer that allows to display several secondary structures on the same drawing using backbone representation [More information on RNAfamily]
You can use Carnac via the web interface.
It is also possible to download and install it locally (carnac.tar.gz and read_me).
You need a C compiler.
A Windows executable is also available in this zip archive .
CARNAC: folding families of non coding RNAs
Touzet H. and Perriquet O.
Nucleic Acids Research 142, 2004 [pubmed]
Finding the common structure shared by two homologous RNAs.
Perriquet O, Touzet H, Dauchet M.
Bioinformatics. 2003 Jan;19(1):108-16 [pubmed]