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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 or Dot-Bracket
file. The output from efn2 can be either a simple list of
energies or a detailed breakdown of the calculation.
efn2 now supports structures that contain pseudoknots (as of
version 6.0).
efn2 now by default reports error estimates for free energy calculations for RNA (as of
version 6.1; this can be disabled using --ne). This is described in Zuber and Mathews (2018).
efn2-smp is a parallel processing version for use on multi-core
computers, built using OpenMP.
Important Note: efn2 uses a different energy
function for estimating multibranch loop initiation free energy
changes than the dynamic programming algorithms, e.g. Allsub,
Fold, partition, and stochastic. The efn2 energy function has an
additional term that penalizes asymmetry in the distribution of
unpaired nucleotides around the loop. Therefore, folding free
energies from efn2 can differ from other programs in
RNAstructure. See the -s, -S, --simple flag below.
USAGE: efn2 <ct file> <energy file> [options]
OR: efn2-smp <ct file> <energy file> [options]
| <ct file> |
The name of a CT file
or Dot-Bracket
file containing the input structure. |
| <energy file> |
The energy file to which output is written.
The energy file can be written in one of two forms:
- Simple List
Lists free energy for each structure, lowest first.
This file type is written by default.
- Thermodynamic Details
Writes details of every substructure in each
structure, and corresponding free energy of each.
This file type is only written if "-w," "-W," or
"--writedetails" (see below) is specified, and
replaces a simple list file.
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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. |
| -h, -H, --help |
Display the usage details message. |
| --ne |
Do not calculate experimental uncertainties. |
| -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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| -s, -S, --simple |
Use the simple energy function for multibranch loops
that is the same used by the dynamic programming
algorithms (Fold, partition, stochastic, AllSub, etc.). If
this is not specified, an more sophisticated energy
function is used, and the energies might not match those
estimated for structures during structure prediction. |
| -w, -W, --writedetails |
Write a thermodynamic details file.
The thermodynamic details file replaces a standard output
(list) file. |
| -a, -A, --alphabet |
Specify the name of a folding alphabet and
associated nearest neighbor parameters. The alphabet is
the prefix for the thermodynamic parameter files, e.g.
"rna" for RNA parameters or "dna" for DNA parameters or a
custom extended/modified alphabet. The thermodynamic
parameters need to reside in the at the location indicated
by environment variable DATAPATH.
The default is "rna" (i.e. use RNA parameters). This
option overrides the --DNA flag. |
| -c, -C, --count |
Specify a file where parameter usage counts will be exported |
| -sh, -SH, --SHAPE |
Specify a SHAPE
constraints file to be applied. These constraints
specificially use SHAPE pseudoenergy constraints.
Default is no SHAPE constraint file specified. |
| -si, -SI, --SHAPEintercept |
Specify an intercept used with SHAPE constraints.
Default is -0.6 kcal/mol. |
| -sm, -SM, --SHAPEslope |
Specify a slope used with SHAPE constraints.
Default is 1.8 kcal/mol. |
| -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. |
efn2-smp, by default, will use all available compute cores for
processing. The number of cores used can be controlled by
setting the OMP_NUM_THREADS environment variable.
- The calculation of uncertainty in folding free energy changes
is only enabled in efn2, not efn2-smp.
- The calculation of uncertainty can only be done for RNA sequences, since the
required data tables are not available for DNA.
- The error estimates calculated by efn2 currently do not take into account uncertainty in the pseudoknot or SHAPE energy models.
- Zuber, J and Mathews, D.H.
"Estimating Uncertainty in Predicted Folding Free Energy Changes of RNA Secondary Structures"
RNA, Submitted. (2018).
- Reuter, J.S. and Mathews, D.H.
"RNAstructure: software for RNA secondary structure prediction
and analysis."
BMC Bioinformatics, 11:129. (2010).
- 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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