RemovePseudoknots takes a structure (or structures) and breaks pairs to generate a pseudoknot-free structure (or structures) with either lowest folding free energy change or with fewest removed pairs.
USAGE: RemovePseudoknots <input ct file> <output ct file> [options]
|<input ct file>
||The name of a CT file possibly containing structure(s) with pseudoknotted pairs.
|<output ct file>
||The name of a pseudoknot-free CT file to which output will be written.
|-d, -D, --DNA
Specify that the sequence is DNA, and DNA parameters are to be used.
Default is to use RNA parameters.
(This has no effect if the -m, -M, --maximize option is chosen.)
|-h, -H, --help
||Display the usage details message.
|-m, -M, --maximize
Specify that remaining base pairs should be maximized in the pseudoknot-free structure.
Default is that the structure(s) should have minimum free energy.
Minimizing free energy change can result in fewer pairs in the pseudoknot free structure(s) than the maximum.
|-t, -T, --temperature
Specify the temperature at which calculation takes place in Kelvin.
Default is 310.15 K, which is 37 degrees C.
Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction and analysis."
BMC Bioinformatics, 11:129. (2010).
Smit, S., Rother, K., Heringa, J. and Knight, R.
"From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal."
RNA, 14:410-416. (2008).