Using the Predict a Secondary Structure Common to Three or More Sequences Server

The Predict a Secondary Structure Common to Three or More Sequences server combines the following algorithms:
  1. Multilign
    Predict low free energy secondary structures common to three or more sequences using progressive iterations of Dynalign.
  2. TurboFold
    Calculate the conserved structures of three or more unaligned sequences using iteratively refined partition functions.

There is a limit to the length of the sequences that can be run through the algorithms used in this server. 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" 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. Change default general data, if desired.

    The Predict a Secondary Structure Common to Three or More Sequences server allows specification of a temperature that can be applied to both Multilign and TurboFold. This value has a default, so it is not necessary to specify the value in order to do calculations.
  3. Change default Multilign data, if desired.

    The Multilign section of the server allows specification of a number of iterations, maxdsvchange, maximum percent energy difference, maximum number of structures, structure window size, alignment window size, and gap penalty. All of these values have defaults, so it is not necessary to specify values in order to do calculations.
  4. Add optional Multilign data, if desired.

    The Multilign section of the server can specify whether or not single base pair inserts are allowed. By default, single base pair inserts are allowed.
  5. Select the TurboFold folding mode.

    The TurboFold section of the 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.
  6. Change default TurboFold data, if desired.

    The TurboFold section of the server allows specification of different options, depending on the mode specified. For general options, the server allows specification of a 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.
  7. Add optional TurboFold data, if desired.

    The TurboFold section of the 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.
  8. 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.
  9. 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 Multilign algorithm and its parameters, please click here.
For detailed explanations of the TurboFold algorithm and its parameters, please click here.