Non-protein-coding RNA detection


A problem? Please consult the Darn manual online.


The selection of a descriptor file will fill in the following text area.

You can edit the content of the text area.

Sequence alignment:

Alternatively, you can paste an multiple alignment in the following text area using the Stockholm format (with the structure), and Darn will build a descriptor for this alignment.

Main sequence:

You can either choose a file in our database, paste your fasta sequence, or upload your fasta file.

Select a sequence file here:


or paste your fasta file here:

or upload a fasta file here (for technical reasons, the file size should not exceed 60 Mo):

Target sequence (if needed by the descriptor):

Only if a duplex motif is given in the descriptor thanks to the T variables. Otherwise, you may get an error.

You may either choose a target in the following database, or paste your fasta sequence.

Select a sequence here:


or paste your fasta file here:


Please select the strand on the main stem you want to scan:

the positive strand

the negative strand

both strands

Please select which direction on the target stem you want to scan:

from 3' to 5'

from 5' to 3'

Use GFF format to output solutions.

Use FASTA format to output solutions.

Give solutions with lower costs first.

Give the costs given by the constraints.

Display secondary structure using parenthesis representation.

Important notice: since this web page is available to anyone, every job is interrupted after 2 minutes, and the solutions found so far are displayed. Please download the software for larger searches.

Download Darn

You can also download a local version of Darn from a Forge.

Last update February 10, 2010.