NAME

       RNAdos - manual page for RNAdos 2.6.4

SYNOPSIS

       RNAdos [OPTIONS]

DESCRIPTION

       RNAdos 2.6.4

       Calculate the density of states for each energy band of an RNA

       The program reads an RNA sequence and computes the density of states for each energy band.

       -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)

   I/O Options:
              Command line options for input and output (pre-)processing

       -s, --sequence=STRING
              The RNA sequence (ACGU).

       -j, --numThreads=INT
              Set the number of threads used for calculations (only available when compiled with OpenMP support)

   Algorithms:
              Select  additional  algorithms  which  should  be  included in the calculations.  The Minimum free
              energy (MFE) and a structure representative are calculated in any case.

       -e, --max-energy=INT
              Structures are only counted until this threshold is reached. Default is 0 kcal/mol.

              (default=`0')

       -b, --hashtable-bits=INT
              Set the size of the hash table for each cell in the dp-matrices.

              (default=`20')

   Energy Parameters:
              Energy parameter sets can be adapted or loaded from user-provided input files

       -T, --temp=DOUBLE
              Rescale energy parameters to a temperature of temp C. Default is 37C.

              (default=`37.0')

       -P, --paramFile=paramfile
              Read energy parameters from paramfile, instead of using the default parameter set.

              Different sets of energy parameters for RNA and DNA should accompany your distribution.   See  the
              RNAlib  documentation  for details on the file format. The placeholder file name 'DNA' can be used
              to load DNA parameters without the need to actually specify any input file.

       --salt=DOUBLE
              Set salt concentration in molar (M). Default is 1.021M.

   Model Details:
              Tweak the energy model and pairing rules additionally using the following parameters

       -d, --dangles=INT
              How to treat "dangling end" energies for bases adjacent to helices in free ends and multi-loops.

              (default=`2')

              With -d1 only unpaired bases can participate in at most one dangling end.  With -d2 this check  is
              ignored,  dangling  energies  will be added for the bases adjacent to a helix on both sides in any
              case; this is the default for mfe and partition function folding (-p).   The  option  -d0  ignores
              dangling ends altogether (mostly for debugging).  With -d3 mfe folding will allow coaxial stacking
              of  adjacent  helices  in  multi-loops.  At  the  moment the implementation will not allow coaxial
              stacking of the two interior pairs in a loop of degree 3 and works only for mfe folding.

              Note that with -d1 and -d3 only the MFE computations will be using this  setting  while  partition
              function uses -d2 setting, i.e. dangling ends will be treated differently.

       --helical-rise=FLOAT
              Set the helical rise of the helix in units of Angstrom.

              (default=`2.8')

              Use with caution! This value will be re-set automatically to 3.4 in case DNA parameters are loaded
              via -P DNA and no further value is provided.

       --backbone-length=FLOAT
              Set the average backbone length for looped regions in units of Angstrom.

              (default=`6.0')

              Use  with  caution!  This  value  will  be re-set automatically to 6.76 in case DNA parameters are
              loaded via -P DNA and no further value is provided.

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

       J. Cupal, I.L. Hofacker, P.F. Stadler (1996), "Dynamic programming algorithm for the density of states of
       RNA secondary structures" Computer Science and Biology 96, Proc. German Conf. on Bioinformatics 1996, pp.
       184-186.

       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

       Gregor Entzian, 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.

SEE ALSO

       RNAsubopt(1)

RNAdos 2.6.4                                      January 2025                                         RNADOS(1)