Welcome to the Predict a Secondary Structure Common to Three or More Sequences Web Server

The Predict a Secondary Structure Common to Three or More Sequences server takes three or more sequences and folds them into their common lowest free energy conformations. The Predict a Secondary Structure Common to Three or More Sequences server combines the capabilities of Multilign and TurboFold to create distinct sets of possible structures for multiple sequences. Note that sequences must be entered as a group in this server. Sequences can be entered either as a FASTA file with multiple sequences, or manually in the sequence box. Note also that the server assumes the sequences are RNA.

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 Predict a Secondary Structure Common to Three or More Sequences 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: (Click here to add example sequences to the box.)

Select General Options:

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

Select Multilign Options:

Default Data If a default value is left blank, the value is treated as if it was not changed at all. Iterations: Maxdsvchange: Maximum % Energy Difference: Maximum Number of Structures: Structure Window Size: Alignment Window Size: Gap Penalty:

Optional Data

Allow Single Base Pair Inserts:

Select TurboFold Options:

Folding Mode

Maximum Expected Accuracy:
Pseudoknots:
Threshold:

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

General Options

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