ProbablePair creates a group of suboptimal structures that contain base pairs above a probability threshold.
USAGE: ProbablePair <input file> <ct file> [options]
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).
||The name of a CT file to which output will be written.
|-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.
||Identify the input file format as a sequence file.
|-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.
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).