Welcome to the Dynalign Web Server

The Dynalign server takes two nucleic acid sequences, either RNA or DNA, and determines common secondary structures. Additionally, it creates an alignment file of the sequences. Both sequences, as well as the resulting alignment, can be restrained using constraint files. Note that if an error is encountered in Dynalign calculation, it may still be possible to fold one or both component sequences independently without errors.

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 Dynalign 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.

Example sequences have been displayed.

Select Sequence 1 Input:

Select Sequence File 1:

- OR -
Enter your sequence title and content below (replaces upload if present).
Please enter nucleotides only, no headers or comments in content.
Valid nucleotides are A, C, G, T, U, and X (unknown nucleotide). Lower case nucleotides are forced single stranded in calculation.

Sequence 1 Title: Sequence 1:

Select Sequence 2:

Select Sequence File 2:

Sequence 2 Title: Sequence 2:

Select Nucleic Acid Type:

DNA:
RNA:

Select Dynalign Options:

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

Optional Data

Allow Single Base Pair Inserts:

Select Folding Constraints File For Sequence 1: Select Folding Constraints File For Sequence 2:

Designate Address to Email Results:

Address to Email Results: