Using the TurboFold Server

There is a limit to the length of the sequences that can be run through the TurboFold algorithm. For details, please click here.
It is possible to input example sequences into the sequence box by clicking on the link above the "Select Sequences Input" form section.

  1. Select sequences for analysis.

    Selection of sequences can be done in one of two ways. First, a sequence file in FASTA format, containing multiple sequences can be uploaded using the "Select Sequences File 1" control. Second, raw sequence data can be input in the "Sequences" box. Please note that each sequence must be in proper FASTA format, with a header on one line before each sequence, and no blank lines or numbers interrupting the sequence itself.

  2. Select the folding mode.

    The TurboFold server can be run in three distinct modes: maximum expected accuracy mode, pseudoknot mode, or threshold mode. By default, the server uses maximum expected accuracy mode.

  3. Change default data, if desired.

    The TurboFold server allows specification of different options, depending on the mode specified. For general options, the server allows specification of a temperature, general gamma, and number of iterations the main folding algorithm will go through. For maximum expected accuracy mode options, the server allows specification of a maximum percent energy difference, maximum number of structures, window size, and mode-specific gamma. For pseudoknots mode options, the server allows specification of a number of iterations in which to find pseudoknots and a minimum helix length. 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 TurboFold server allows specification of different options, depending on the mode specified. For general options, the server allows specification of a maximum pairing distance.. For threshold mode options, the server allows specification of a threshold cutoff.

  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 TurboFold algorithm and its parameters, please click here.