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RNAstructure Command Line Help

CycleFold predicts both canonical and non-canonical base pairs using nucleotide cyclic motifs (Parisien & Major, 2008). It predicts either lowest free energy structures or base pairing probabilities.

By default, the minimum free energy structure is predicted. The options, below, can change the behavior to predicting base pair probabilities or using predicted base pair probabilities to predict the maximum expected accuracy structure. If multiple sequences are entered, the TurboFold mode can also be specified. All output is to standard out.

CycleFold requires the environment variable, CYCLEFOLD_DATAPATH, be set to the location of the datatables, which reside in RNAstructure/CycleFold/datafiles.

USAGE: CycleFold <seq file> [options]


Required parameters:

<seq file> The name of a fasta file that contains the sequence.

Options that do not require added values:

-b, -B, --bigloops Allow large internal loops or hairpin loops, whose energies are not tabulated in the NCM model. This is sometimes necessary for structure calculations with constraints (-c or -ct opions).
-fc, -FC, --fastaConstraints Specify that the input fasta file contains secondary structure constraints (in dot-bracket format) to be applied to each structure.
Default: off.
-h, -H, --help Display the usage details message.
-m, -M, --maxExpect Specify that a MaxExpect calculation should be performed. (This predicts a structure composed of probable base pairs.)
-p, -P, --partitionfunction Specify that pair probabilities should be printed.
-s, -S, --seqFormat Switch the expected input from FASTA to .seq format.
-t, -T, --turbo Specify that a TurboFold calculation should be performed. TurboFold writes all of the structures or pair probability tables, with their labels, in the order that they were provided.
-u, -U, --unpairingConstraints Toggle whether restraints should be treated as unpairing constraints.
Default: off.
-v, -V, --version Display the version and copyright information.

Options that require added values:

-c, -C, --constraintFile

Specify a constraint file to be applied (in constraint file format).
Default is to have no constraints applied.

-ct, -CT, --constrainCt Specify a constraint file to be applied (in ct format).
-g, -G, --gamma Set gamma, the weighting parameter for extrinsic information in the
turbo calculation. The default is 0.6.
-i, -I, --iterations Set the number of iterations for the turbo calculation. The default is 2.



Unlike most other programs in RNAstructure, lowercase nucleotides are allowed to base pair.


  1. Reuter, J.S. and Mathews, D.H.
    "RNAstructure: software for RNA secondary structure prediction and analysis."
    BMC Bioinformatics, 11:129. (2010).
  2. Sloma, M.F. and Mathews, D.H.
    "Accurate prediction of RNA non-canonical pairs using probability estimates."
    In review.
  3. Parisien, M. and Major, F.
    "The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data."
    Nature, 452: 51-55. (2008).