RNAparconv
RNAparconv - manual page for RNAparconv 2.6.4
Synopsis
RNAparconv [options] [<input file>] [<output file>]
DESCRIPTION
RNAparconv 2.6.4
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
I/O Options:
Command line options for input and output (pre-)processing
- -i, --input=filename
Specify an input file name. If argument is missing the energy parameter input can be supplied via
stdin.
- -o, --output=filename
Specify an output file name. If argument is missing the converted energy parameters are printed to
stdout.
- --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)
REFERENCES
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
REPORTING BUGS
If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.