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 predicts their common secondary structures. The Predict a Secondary Structure Common to Three or More Sequences server combines the capabilities of Multilign and TurboFold to create distinct sets of predicted structures. These two predictions represent alternative hypotheses. Generally, Multilign is more accurate when the sequence identities are low (<30%). Also, the TurboFold alignments are generally more accurate; Multilign aligns sequences based on structure and does not consider nucleotide identities. 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.

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If you need specific help using the Predict a Secondary Structure Common to Three or More Sequences server, please click here.

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RNAstructure tools have been updated to version 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 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