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]
The name of a file containing input data. This input data can be in one of three formats:
- Partition function save file (holds base pairing probability data for all pairs and can be generated using the partition interface).
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).
- ct file (holds a set of structures). This should be a stochastic sample. (see "--ensemble") 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 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.
||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.
||Identify the input file format as a sequence file.
|-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.
Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction and analysis."
BMC Bioinformatics, 11:129. (2010).
Bellaousov, S., and Mathews, D.H.
"ProbKnot: fast prediction of RNA secondary structure including pseudoknots."
RNA, 16:1870-1880. (2010).
- Zhang, L., Zhang, H., Mathews, D.H, andHuang, L.
"ThreshKnot: Thresholded Probknot for Improved RNA Secondary Structure Prediction."