Welcome to the PARTS Web Server

The PARTS server takes two RNA sequences and estimates the common secondary structure. Additionally, it creates an alignment file of the sequences. PARTS can be run in one of three modes: pairing probability (PP) mode, maximum a posteriori (MAP) mode, or stochastic sampling mode.

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 PARTS 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.

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 Folding Mode:

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

Select PARTS Options:

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: