Using the Predict a Secondary Structure Server

The Predict a Secondary Structure server combines the following algorithms:
  1. partition
    Perform a partition function calculation on a single sequence to calculate base pair probabilities.
  2. Fold
    Predict the lowest free energy structure in a set of low free energy structures for a sequence.
  3. MaxExpect
    Generate a structure or structures composed of highly probable base pairs.
  4. ProbKnot
    Predict a secondary structure of probable base pairs, including pseudoknots.

There is a limit to the length of the sequence that can be run through the algorithms used in this server. 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.

    The Predict a Secondary Structure server allows upload of a sequence file in FASTA format using the "Select Sequence File" control.
    The Predict a Secondary Structure server also allows raw sequence data to be input in the "Sequence" box. It is possible to input an example sequence into the box by clicking on the link next to the "Sequence" label. 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 Predict a Secondary Structure server allows specification of a temperature, maximum percent energy difference, maximum number of structures, window size, and gamma. All of these values have defaults, so it is not necessary to specify values in order to do calculations.

  4. Add optional data, if desired.

    The Predict a Secondary Structure server allows specification of a folding constraints file if folding should be restricted in some way. By default, no folding constraints file is specified. A folding constraints file is not required in order to do calculations.
    The Predict a Secondary Structure server also allows specification of SHAPE data, namely, a SHAPE constraints file, SHAPE intercept, and SHAPE slope. By default, no SHAPE constraints file is specified. A SHAPE constraints file is not required in order to do calculations. The values for SHAPE intercept and SHAPE slope have defaults, so it is not necessary to specify values in order to do calculations. Note that SHAPE intercept and SHAPE slope are never applied unless a SHAPE constraints file is specified.

  5. 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.

  6. 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 partition algorithm and its parameters, please click here.
For detailed explanations of the Fold algorithm and its parameters, please click here.
For detailed explanations of the MaxExpect algorithm and its parameters, please click here.
For detailed explanations of the ProbKnot algorithm and its parameters, please click here.