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.

Select Sequence 1 Input:

- 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.




Select Sequence 2:

- 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.




Select Nucleic Acid Type:




Select Dynalign Options:

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




Designate Address to Email Results: