Welcome to the partition Web Server

The partition server takes a sequence file of nucleic acids, either DNA or RNA, and calculates its partition function. A wide variety of constraints can be applied, including, but not limited to, pairing restraints, modifications, and addition of SHAPE data. The partition function is often used to measure the probability of pairs forming in a structure, and by extension, the quality of the structure which contains those pairs.

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 partition server, please click here.

Note: The maximum sequence length has been increased for several tools. Please see Sequence Limits for details.

Select Sequence 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 Nucleic Acid Type:




Select partition Options:

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



Specify the minimum and maximum probabilities to show on the dot plot.
If a specified probability is out of range, it is ignored.


Note that in order to use SHAPE intercept and/or SHAPE slope, a SHAPE constraints file must be specified. If a value is given for intercept or slope without an accompanying constraints file, the intercept or slope value is not used in calculation.



Designate Address to Email Results: