Using the Predict a Secondary Structure Common to Two Sequences Server

The Predict a Secondary Structure Common to Two Sequences server combines the following algorithms:
  1. Dynalign
    Calculate the lowest free energy secondary structures common to two unaligned sequences.
  2. PARTS
    Predict the common secondary structure, including base pair probabilities, for two unaligned sequences.

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 a first 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 1" control. Second, raw sequence data can be input in the "Sequence 1" 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 1" box.

  2. Select a second 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 2" control. Second, raw sequence data can be input in the "Sequence 2" 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 2" box.

  3. Change Dynalign default data, if desired.

    The Dynalign section of the server allows specification of a 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 Dynalign optional data, if desired.

    The Dynalign section of the server can specify whether or not single base pair inserts are allowed. By default, single base pair inserts are allowed. The server also allows specification of a folding constraints file for sequence 1 and/or a folding constraints file for sequence 2 if folding should be restricted in some way. By default, no constraints files are specified. No constraints files are required in order to do calculations.

  5. Select the PARTS folding mode.

    The PARTS section of the server can be run in three distinct modes: MAP (maximum a posteriori) prediction mode, pairing probability prediction mode, or stochastic sampling mode. By default, the server uses MAP (maximum a posteriori) prediction mode.

  6. Change PARTS default data, if desired.

    The PARTS section of the server allows specification of a number of structures, but this is applicable in stochastic sampling mode only. It has a default filled in, however, so it is not necessary to change it in order to do calculations.

  7. Add PARTS optional data, if desired.

    The PARTS section of the server allows specification of a minimum plot bound and maximum plot bound. Neither of these values have defaults, and it is not necessary to specify values in order to do calculations.

  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 Dynalign algorithm and its parameters, please click here.
For detailed explanations of the PARTS algorithm and its parameters, please click here.