Using the Fold Server

There is a limit to the length of the sequence that can be run through the Fold 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 Fold server allows specification of a maximum percent energy difference, maximum number of structures, window size, maximum loop size, and temperature. 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 Fold server allows specification of a folding constraints file if folding should be restricted in some way. By default, no constraints file is specified. A constraints file is not required in order to do calculations. The Fold server also allows specification of SHAPE data, namely, a SHAPE constraints file, SHAPE intercept, and SHAPE slope.. The values for SHAPE intercept and SHAPE slope have defaults, but by default no constraints file is specified. None of the values are required 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 Fold algorithm and its parameters, please click here.