NAME

       RNAdos - manual page for RNAdos 2.4.17

SYNOPSIS

       RNAdos [OPTIONS]

DESCRIPTION

       RNAdos 2.4.17

       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

       -V, --version
              Print version and exit

   General Options:
              Command line options which alter the general behavior of this program

       -v, --verbose
              Be verbose.

              (default=off)

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

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

              (default=`0')

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

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

       -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.

       -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. When passing the placeholder file name "DNA",
              DNA parameters are loaded without the need to actually specify any input file.

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

              (default=`20')

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)