Welcome to the Predict a Secondary Structure Common to Two Sequences Web Server

The Predict a Secondary Structure Common to Two Sequences server takes two sequences, determines common secondary structures, and and calculates base pair probabilities. Additionally, it creates two alignment files of the sequences. Both sequences, as well as the resulting alignments, can be restrained using constraint files. Note that if an error is encountered in calculations, it may still be possible to do other calculations on one or both component sequences independently without errors. 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 Two 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.

Click here to add an example sequence to both sequence boxes.

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 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:

Select PARTS Options:

Mode

MAP (Maximum A Posteriori) Prediction:
Pairing Probability Prediction:
Stochastic Sampling:

Default Data If a default value is left blank, the value is treated as if it was not changed at all. Number of Structures (Applies in Stochastic Sampling Mode Only):

Optional Data Specify the minimum and maximum probabilities to show on the dot plot.
If a specified probability is out of range, it is ignored. Minimum (Applies in Pairing Probability Prediction Mode Only): Maximum (Applies in Pairing Probability Prediction Mode Only):

Designate Address to Email Results:

Address to Email Results: