RNAparconv - manual page for RNAparconv 2.5.1
RNAparconv [
options] [
<input file>] [
<output
file>]
RNAparconv 2.5.1
Convert energy parameter files from ViennaRNA 1.8.4 to 2.0 format
Converts energy parameter files from "old" ViennaRNAPackage 1.8.4
format to the new format used since ViennaRNAPackage 2.0. The Program reads a
valid energy parameter file or valid energy parameters from stdin and prints
the converted energy parameters to stdout or a specified output file. Per
default, the converted output file contains the whole set of energy parameters
used throughout ViennaRNAPackage 1.8.4. The user can specify sets of energy
parameters that should not be included in the output.
-
-h, --help
- Print help and exit
- --full-help
- Print help, including hidden options, and exit
-
-V, --version
- Print version and exit
-
-o, --output=filename
- Specify an output file name. If argument is missing the
converted energy parameters are printed to 'stdout'.
-
-i, --input=filename
- Specify an input file name. If argument is missing the
energy parameter input can be supplied via 'stdin'.
- --vanilla
- Print just as much as needed to represent the given energy
parameters data set. This option overrides all other output settings!
- (default=off)
- --dump
- Just dump Vienna 1.8.4 energy parameters in format used
since 2.0. This option skips any energy parameter input!
- (default=off)
- --silent
- Print just energy parameters and appropriate comment lines
but suppress all other output
- (default=off)
- --without-HairpinE
- Do not print converted hairpin energies and enthalpies
- (default=off)
- --without-StackE
- Do not print converted stacking energies and
enthalpies
- (default=off)
- --without-IntE
- Do not print converted interior loop energies, enthalpies
and asymetry factors
- (default=off)
- --without-BulgeE
- Do not print converted bulge loop energies and
enthalpies
- (default=off)
- --without-MultiE
- Do not print converted multi loop energies and
enthalpies
- (default=off)
- --without-MismatchE
- Do not print converted exterior loop mismatch energies and
enthalpies
- (default=off)
- --without-MismatchH
- Do not print converted hairpin mismatch energies and
enthalpies
- (default=off)
- --without-MismatchI
- Do not print converted interior loop mismatch energies and
enthalpies
- (default=off)
- --without-MismatchM
- Do not print converted multi loop mismatch energies and
enthalpies
- (default=off)
- --without-Dangle5
- Do not print converted 5' dangle energies and
enthalpies
- (default=off)
- --without-Dangle3
- Do not print converted 3' dangle energies and
enthalpies
- (default=off)
- --without-Misc
- Do not print converted Misc energies and enthalpies
(TerminalAU, DuplexInit, lxc)
- (default=off)
If you use this program in your work you might want to cite:
R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F.
Stadler and I.L. Hofacker (2011), "ViennaRNA Package 2.0",
Algorithms for Molecular Biology: 6:26
I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster
(1994), "Fast Folding and Comparison of RNA Secondary Structures",
Monatshefte f. Chemie: 125, pp 167-188
R. Lorenz, I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and
soft constraints", Algorithms for Molecular Biology 11:1 pp 1-13
The energy parameters are taken from:
D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M.
Zuker, D.H. Turner (2004), "Incorporating chemical modification
constraints into a dynamic programming algorithm for prediction of RNA
secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292
D.H Turner, D.H. Mathews (2009), "NNDB: The nearest neighbor parameter
database for predicting stability of nucleic acid secondary structure",
Nucleic Acids Research: 38, pp 280-282
Ronny Lorenz
If in doubt our program is right, nature is at fault. Comments should be sent to
[email protected].