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)