Vienna RNA Secondary Structure Prediction

A web interface to the RNAfold programm

This server will predict secondary structures of single stranded RNA or DNA sequences. If the options look confusing read the help page

News: based on ViennaRNA-1.5
Try the new SVG plot if your browser supports it!
You can now submit sequences up to 4000 as batch jobs. for the cgi
Type in your sequence Ts will be automatically replaced by Us. Any symbols except AUCGTXKI will be interpreted as nonbonding bases. Any non-alphabetic characters will be removed.

Maximum sequence length for immediate jobs is 300. Sequences up to 4000 (mfe only) or 3000 (pair probabilities) will be queued as batch jobs

Choose Fold Algorithm

Options to modify the fold algorithm

Rescale energy parameters to temperature C

no special tetraloops
no dangling end energies
no GU pairs at the end of helices
avoid isolated base pairs

Should we produce a mountain plot of the structure? plot
View a plot of the mfe structure inline using an SVG image (may require plugin) SVG
or using the SStructView java applet? SSview
Email address. For batch jobs (over 300) this is mandatory, so we can notify you when the job has completed.

We appreciate your feedback. Please send comments to
Ivo Hofacker <>

Vienna RNA Home Page