To run an MC-Fold batch job, please upload a text file containing the sequences in the FASTA format.

Lines can be commented out by starting it with a "#".

Different parameters can be set to each sequence. This can be achieved by adding the parameters under each sequence following this syntax: [parameter]<whitespace(s)>[value]. The applicable parameters varies between the different versions of MC-Fold, please refer to the sections below to get descriptions for each parameter.

Parameters for MC-Fold 1.6.0

  • top: The number of structures returned by MC-Fold.
  • explore: Percentage of the best candidates that will be explored by MC-Fold.
  • mask: Structural mask that will be applied to the sequence.
  • singlehigh: Single-Stranded Chemical/Enzymatic Reactivity Data (+8 kcal/mol penalty).
  • singlemed: Single-Stranded Chemical/Enzymatic Reactivity Data (+4 kcal/mol penalty).
  • singlelow: Single-Stranded Chemical/Enzymatic Reactivity Data (+2 kcal/mol penalty).
  • sequence2: Annealed sequence.
  • pseudoknots: Consider H-Type Pseudoknots (value can be either "true" or "false").

    • Parameters for MC-Fold 2.2.3 (beta)

  • top: The number of structures returned by MC-Fold.
  • mask: Structural mask that will be applied to the sequence. (Note: If you define a mask, you also have to define the mask_type parameter)
    • mask_type: The category of mask that will be applied. (value can be either "balanced" or "unbalanced")
  • graph: Compute the graph of disconected components

    • Please find an example of an MC-Fold Batch input file below: