You may use the CONTRAfold server to predict RNA secondary structures. Input to the server consists of a single FASTA format sequence, up to 1000 characters in length.

For larger sequences, CONTRAfold may be executed on your local machine (see download page). (See the FAQ for a note regarding multiple sequence prediction with CONTRAfold.)

The email server is currently down. Please use the web interface.

Step 1: Choose either of two input methods.

(a) Enter FASTA format sequence (see example)


(b) Upload FASTA format text file:

Step 2: Choose either of two output methods.

Send results to e-mail address:

Type your e-mail address:  
Re-type your e-mail address:  


Send results to web browser.

Step 3: Select advanced options (optional).

Output format:   Parenthesized
Base-pairing:   Allow only complementary base pairs (AU, CG, GU)
Allow all possible base pairs

Step 3: Click submit!