Welcome to the TurboFold Web Server

The TurboFold server takes three or more RNA sequences and folds them into their common lowest free energy conformations, as well as calculates base pairing probabilities and a multiple-sequence alignment file. It does this by generating pairwise alignments between sequences using a hidden markov model (HMM), which supplies extrinsic information to one of three selectable folding modes. The alignments and folding output are iteratively used to improve each other.

The sequences should be combined in a single FASTA file or they can be manually entered in the sequence box below. In either case, the format should be similar to the following:

> RA7680 (Name of Sequence 1)
GGGGGCGUAG CUCAGAuGGU AGAGCGCUCG CUUgGCgUGU GAGAGGUACC GGGAUCGaUA CCCGGCGCCU CCACCA
> RD0260 (Name of Sequence 2)
GCGACCGGGG CUGGCUUGGU AAUGGUACUC CCCUGUCACG GGAGAGAAUG UGGGUUCAAA UCCCAUCGGU CGCGCCA
> RD0500 (Name of Sequence 3)
GCCCGGGUGG UGUAGUGGCC CAUCAUACGA CCCUGUCACG GUCGUGACGC GGGUUCgAAU CCCGCCUCGG GCGCCA
(... Additional Sequences)

Note that sequences can contain white-space (spaces, tabs and line-breaks). Lowercase letters are forced to be unpaired (single-stranded).

If you plan to leave this page while waiting for calculations to complete, please make sure you have entered a valid email address below. Leaving this page without entering a valid email address will render results inaccessible.

If you need specific help using the TurboFold server, please click here.

February 14, 2018:
RNAstructure tools have been updated to version 6.0.1 which includes several improvements.
Please contact us with any questions or issues regarding this update.

Select Sequences Input:

Select Sequences File:

- OR -
Enter your sequence content below (replaces upload if present).
Sequence content should be entered in FASTA format, with a proper FASTA header on a line preceding each sequence.
Please enter headers and nucleotides only, no comments in content.
Valid nucleotides are A, C, G, T, U, and X (unknown nucleotide). Lower case nucleotides are forced single stranded in calculation.

Sequences: (Example sequences have been displayed.)

> RA7680
GGGGGCGUAG CUCAGAuGGU AGAGCGCUCG CUUgGCgUGU GAGAGGUACC GGGAUCGaUA CCCGGCGCCU CCACCA
> RD0260
GCGACCGGGG CUGGCUUGGU AAUGGUACUC CCCUGUCACG GGAGAGAAUG UGGGUUCAAA UCCCAUCGGU CGCGCCA
> RD0500
GCCCGGGUGG UGUAGUGGCC CAUCAUACGA CCCUGUCACG GUCGUGACGC GGGUUCgAAU CCCGCCUCGG GCGCCA

Select Folding Mode:

Maximum Expected Accuracy:
Pseudoknots:
Threshold:

Select Alignment File Output Format:

Clustal:
FASTA:

Select TurboFold Options:

Default Data If a default value is left blank, the value is treated as if it was not changed at all.

General Options

Temperature: TurboFold Gamma: TurboFold Iterations:

Maximum Expected Accuracy Mode Options

Maximum % Energy Difference: Maximum Number of Structures: Window Size: Maximum Expected Accuracy Gamma:

Pseudoknots Mode Options

Pseudoknot Iterations: Minimum Helix Length:

Optional Data

Threshold Mode Options

Threshold:

Designate Address to Email Results:

Address to Email Results:

RNAstructure

Web Servers for RNA Secondary Structure Prediction