RNAstructure Help
RemovePseudoknots

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RemovePseudoknots takes a structure and breaks pairs to generate a pseudoknot-free structure with lowest folding free energy change.

USAGE: RemovePseudoknots <input ct file> <output ct file> [options]

Required parameters:

<input ct file>	The name of a file containing pseudoknotted structure data in ct format.
<output ct file>	The name of a pseudoknot-free CT file to which output will be written.

Options which don't require added values:

-d, -D, --DNA	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.

Options which require added values:

-t, -T, --temperature

Specify the temperature at which calculation takes place in Kelvin.
Default is 310.15 K, which is 37 degrees C.

References

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)

RNAstructure Help RemovePseudoknots