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ProbKnot is used to predict a maximum expected accuracy structure that can contain pseudoknots. This program also implements ThreshKnot, which incorporates a pair probability threshold. To use the ThreshKnot approach, specifiy a threshold > 0.

USAGE: ProbKnot <input file> <ct file> [options]

Required parameters:

<input file> The name of a file containing input data. This input data can be in one of three formats:
  1. Partition function save file (holds base pairing probability data for all pairs and can be generated using the partition interface).
  2. Sequence file (holds raw sequence: .seq or .fasta).
    Note that lowercase nucleotides are forced single-stranded in structure prediction.
    Note that in order to use a squence file, the "sequence" flag must be specified (see "--sequence" below).
  3. ct file (holds a set of structures). This should be a stochastic sample. (see "--ensemble") below.
<ct file> The name of a CT file to which output will be written.

Options that do not require added values:

-d, -D, --DNA This flag only matters if the input file is a squence file and has been identified as such (see "--sequence" below).
Specify that the sequence is DNA, and DNA parameters are to be used.
Default is to use RNA parameters.
--ensemble Read a ct file of a stochastic sample as the input of the program. The base pairing probabilities for each pair are the calculated from the fraction of structures with that pair.
-h, -H, --help Display the usage details message.
--sequence Identify the input file format as a sequence file.

Options that require added values:

-i, -I, --iterations Specify the number of iterations the calculation will undergo. More iterations can result in more predicted pairs, although a single iteration is generally sufficient.
Default is 1 iteration.
-m, -M, --minimum Specify the minimum length accepted for a helix. A post-processing filter removes short helices.
Default is 3 base pairs.
-t, -T, --threshold Specify a pair probability threshold. Pairs must exceed this threshold (>threshold) to be included in the prediction. This needs to be less than 1.0.
Default is 0.0.


  1. Reuter, J.S. and Mathews, D.H.
    "RNAstructure: software for RNA secondary structure prediction and analysis."
    BMC Bioinformatics, 11:129. (2010).
  2. Bellaousov, S., and Mathews, D.H.
    "ProbKnot: fast prediction of RNA secondary structure including pseudoknots."
    RNA, 16:1870-1880. (2010).
  3. Zhang, L., Zhang, H., Mathews, D.H, andHuang, L.
    "ThreshKnot: Thresholded Probknot for Improved RNA Secondary Structure Prediction."
    In preparation.(2019)