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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.)
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| -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.
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| -t, -T, --temperature |
Specify the temperature at which calculation takes place in Kelvin.
Default is 310.15 K, which is 37 degrees C.
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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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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).
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