NAME

SYNOPSIS

DESCRIPTION

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)

REFERENCES

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

AUTHOR

REPORTING BUGS