This page is a manual for the web server of Carnac.

Submission form

Your data set should include at least two distinct RNA sequences, and sequences should be in FASTA format.

Lower-case and upper-case letters are both accepted. The full standard IUPAC nucleic acid code is not supported: only A, C, G, T and U symbols are recognized. Numerical digits 0, ..., 9, - and dot . symbols are accepted. They are simply ignored by Carnac.

Carnac offers several parameters that determine the final predictions. The most reasonable choice is to use default values. This choice leads to the most reliable results in average.

Apply GC content correction
This option allows to use a variable energy threshold when selecting stems in the secondary structure. Default: checked.

Eliminate redundant sequences
This option allows to discard sequences that are very similar (more than 98% of identity) and that do not bring any further evolutionary information. Default: checked.

Ouput files

For each sequence, Carnac computes a putative secondary structure. The result is stored in four formats: CT, JPG, dot-bracket, and as a list of contrained base pairings. JPG and PS files are both automatically produced from the CT file using NAview. It is also possible to visualize all structures in the same window with the home-made Java applet RNAfamily.

If no structure is detected, then the message No structure found is displayed.

CT (Connectivity Table) - this text file contains the nucleic acids sequence and base pairing information in the form of a list of positions.

JPG - this is a 2D representation of the structure produced with Naview.

Dot-bracket format - This text file encodes a sequence and its secondary structure. Teh first line is a FASTA-like header. The second line contains the sequence. The third line contains the secondary structure: "." is for an unpaired nucleotide, "(" is for a nucleotide that is 5' in a pair, and ")" is for a nucleotide that is paired in 3'.

List of constraints - this file describes the structure as a set of initial contraints for external programs, such as Kinefold or Mfold. Each line corresponds to one helix: F i j k forces the formation of base pairs i.j, i+1.j-1, ... , i+k-1.j-k+1.


This is a multiple alignment of the sequences that hightlights the consensus secondary structure found by Carnac. This aligmnent is built with gardenia.

Download all files

It is also possible to download an archive storing all result files (ct, jpg, dot-bracket and constraints).

Retrieve result with an ID

Each job is assigned an identifier, that allows to retrieve folding results. Files are stored for 24h after job submission.