| ## RNAstructure Command Line Help ProbablePair | ### Contents ### Index
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: Partition function save file (holds base pairing probability data for all pairs and can be generated using partition). 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.
### References: Reuter, J.S. and Mathews, D.H. "RNAstructure: software for RNA secondary structure prediction and analysis." BMC Bioinformatics, 11:129. (2010). 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).