Using the Multilign Server

There is a limit to the length of the sequences that can be run through the Multilign 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 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 Multilign server allows specification of a number of iterations, maxdsvchange, maximum percent energy difference, maximum number of structures, structure window size, alignment window size, gap penalty, 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 Multilign server can specify whether or not single base pair inserts are allowed. By default, single base pair inserts are allowed.
  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 Multilign algorithm and its parameters, please click here.