HotKnots input:

Sequence:
A string containing the letters A, C, G, U, or T, representing the bases Adenine, Cytosine, Guanine, Uracil, and Thymine, respectively. Lower case letters (a, c, g, u, or t) are accepted. Spaces may be inserted between the characters and will be removed when the calculation is performed. The left end of the sequence corresponds to the 5' end of the strand. To keep the load on our server manageable and response times reasonably low, we limit the length of HotKnots's inputs to 100 nucleotides.

Temperature:
Currently, the temperature is fixed to 37°C.

Model and parameters:
Currently, HotKnots use the Dirks and Pierce (DP) and Cao and Chen (CC) models, with the initial parameters (DP03 for DP and CC06 for CC) and with new parameters. Details are provided in "Andronescu, M., Pop, C., and Condon, A., Improved energy parameters for RNA pseudoknotted secondary structure prediction, submitted for publication.". Data and results obtained in this paper can be downloaded from here.

Get results ...:
The user can choose whether to view the output on a dynamically generated web page, or to receive the output via email, or both, by clicking one or both of the "as web page" and "via e-mail" boxes. If a computation takes more than 1 minute, the web interface notifies the user that the result will be sent out only via e-mail. The user must enter an email address in the box provided, in order to get the output via email.

HotKnots output:

HotKnots returns the estimated optimal and suboptimal secondary structures and free energy changes predicted using the selected model and parameters.

Each structure is output using dot-parentheses notation, in which a matching pair of parentheses/brackets/braces denotes a base pair and a dot denotes an unpaired base. The structure is presented below the corresponding pair of strands, and the structure symbols are aligned with the corresponding base in the strand. The structure can be visualized by using the Pseudoviewer web page or software.

Query ID:
Identifier of the query - this is primarily used for maintainance and debugging purposes.

Send these results by e-mail to ...:
Allows the user to send out the results via e-mail (primarily to themselves). Specify only one e-mail address in the field and press the "Send" button to send out the e-mail version of the results webpage.