NAME

       RNAparconv - manual page for RNAparconv 2.5.1

SYNOPSIS

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

DESCRIPTION

       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)

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.