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efn2 (Energy Function 2) is used to calculate the folding free
energy change of a structure or structures in a CT file. The
output from efn2 can be either a simple list of energies or a
detailed breakdown of the calculation. efn2 does not support structures that contain pseudoknots.
USAGE: efn2 <ct file> <energy file> [options]
| <ct file> |
The name of a file containing the input structure in CT format.
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| <energy file> |
The energy file to which output is written.
The energy file can be written in one of two forms:
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Simple List
Lists free energy for each structure, lowest first.
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Thermodynamic details
(if -w, -W, --writedetails is specified as described below)
Writes the details of every substructure in each structure,
and corresponding free energy of each.
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| -d, -D, --DNA |
Specify that the sequence is DNA, and DNA parameters are to
be used.
Default is to use RNA parameters.
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| -h, -H, --help |
Display the usage details message. |
| -p, -P, --print |
Print the output file to standard output.
This won't override default behavior of writing to a file.
Thermodynamic files (if written) are not printed, even if
this option is specified, because they can be very large.
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| -w, -W, --writedetails |
Write a thermodynamic details file.
The thermodynamic details file replaces a standard output
(list) file.
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| -t, -T, --temperature |
Specify the temperature at which the free energy free should be calculated 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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Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H.
"Expanded sequence dependence of thermodynamic parameters
provides improved prediction of RNA secondary structure."
J. Mol. Biol., 288:911-940. (1999). |
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