RNAparconv — ViennaRNA Package

# RNAparconv

RNAparconv - manual page for RNAparconv 2.7.2

## Synopsis

    RNAparconv [options] [<input file>] [<output file>]

## DESCRIPTION

RNAparconv 2.7.2

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

--detailed-help

  Print help, including all details and hidden options, and exit

--full-help

  Print help, including hidden options, and exit

-V, --version

  Print version and exit

-v, --verbose

  Be verbose. (default=off)

  Lower the log level setting such that even INFO messages are passed through.

### 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 internal 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 internal 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)

--log-level=level

  Set log level threshold. (default=”2”)

  By default, any log messages are filtered such that only warnings (level 2) or errors (level 3) are printed. This setting allows for specifying the log level threshold, where higher values result in fewer information. Log-level 5 turns off all messages, even errors and other critical information.

--log-file[=filename]

  Print log messages to a file instead of stderr. (default=”RNAparconv.log”)

--log-time

  Include time stamp in log messages.

  (default=off)

--log-call

  Include file and line of log calling function.

  (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

## AUTHOR

Ronny Lorenz

## REPORTING BUGS

If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.