Using the ProbKnot Server

There is a limit to the length of the sequence that can be run through the ProbKnot algorithm. For details, please click here.
It is possible to input an example sequence into the box by clicking on the link next to the "Sequence" label.

  1. Select a sequence for analysis.

    Selection of a sequence can be done in one of two ways. First, a sequence file in FASTA format can be uploaded using the "Select Sequence File" control. Second, raw sequence data can be input in the "Sequence" box. Please note that only nucleotides (A, C, G, T, U, or X) should be entered in this box, and lower case nucleotides are forced single stranded. If raw sequence data is specified, a sequence title must be specified with it in the "Sequence Title" box.
  2. Select the nucleic acid type.

    By default, the server assumes analysis is of RNA. DNA can be specified by clicking the "DNA" button.
  3. Change default data, if desired.

    The ProbKnot server allows specification of a number of iterations and minimum helix length. This value has a default, so it is not necessary to specify the value in order to do calculations.
  4. Enter an email address where results can be sent, if desired.

    If an email address is specified in the appropriate box, an email will be sent to inform you when calculations are done. Note that failing to enter an email address may cause results to be inaccessible, if you navigate away from the server while calculations are running.
  5. Begin the calculation.

    Press the "Submit Query" button to begin the calculation. If you remain on the server page, the results will appear when they are finished.

For detailed explanations of the ProbKnot algorithm and its parameters, please click here.