RNAstructure logo

RNAstructure Command Line Help

ProbablePair creates a group of suboptimal structures that contain base pairs above a probability threshold.

USAGE: ProbablePair <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 two formats:
  1. Partition function save file (holds base pairing probability data for all pairs and can be generated using partition).
  2. Sequence file (holds 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).
<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 sequence 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.
-h, -H, --help Display the usage details message.
--sequence Identify the input file format as a sequence file.

Options that require added values:

-t, -T, --threshold Specify the pairing threshold for pairs to be included.
This should be expressed as a number >= 0.5 and <= 1.
Default is 0, which signifies structures should be generated at multiple thresholds: 0.99, 0.97, 0.95, 0.90, 0.80, 0.70, 0.60, and 0.50.


  1. Reuter, J.S. and Mathews, D.H.
    "RNAstructure: software for RNA secondary structure prediction and analysis."
    BMC Bioinformatics, 11:129. (2010).
  2. Mathews, D.H.
    "Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization."
    RNA, 10:1178-1190. (2004).