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ProbKnot is used to predict a maximum expected accuracy structure that can contain pseudoknots.
USAGE: ProbKnot <input file> <ct file> [options]
| <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)
-
Sequence file (holds a sequence: .seq or .fasta)
Note that in order to use a sequence file, the "sequence"
flag must be specified (see "--sequence" below).
|
| <ct file> |
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.
|
| -h, -H, --help |
Display the usage details message. |
| --sequence |
Identify the input file 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.
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Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
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Bellaousov, S., and Mathews, D.H.
"ProbKnot: Fast Prediction of RNA Secondary Structure Including Pseudoknots."
Submitted.
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