NAME

       RNAduplex - manual page for RNAduplex 2.6.4

SYNOPSIS

       RNAduplex [OPTION]...

DESCRIPTION

       RNAduplex 2.6.4

       Compute the structure upon hybridization of two RNA strands

       reads  two  RNA  sequences  from  stdin  or <filename> and computes optimal and suboptimal
       secondary structures for their hybridization. The calculation is  simplified  by  allowing
       only inter-molecular base pairs, for the general case use RNAcofold.  The computed optimal
       and suboptimal structure are written to stdout, one structure per line. Each line  consist
       of:  The  structure in dot bracket format with a '&' separating the two strands. The range
       of the structure in the two sequences in the format  "from,to : from,to";  the  energy  of
       duplex  structure  in  kcal/mol.  The format is especially useful for computing the hybrid
       structure between a small probe sequence and a long target sequence.

       -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

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

       -s, --sorted
              Sort the printed output by free energy.

              (default=off)

       --noconv
              Do not automatically substitute nucleotide "T" with "U".

              (default=off)

   Algorithms:
              Select additional algorithms which should be included in the calculations.

       -e, --deltaEnergy=range
              Compute suboptimal structures with  energy  in  a  certain  range  of  the  optimum
              (kcal/mol).  Default is calculation of mfe structure only.

   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.

       -4, --noTetra
              Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop
              hairpins.

              (default=off)

              Mostly for testing.

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

       --saltInit=DOUBLE
              Provide salt correction for duplex initialization (in kcal/mol).

   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.

       --noLP Produce structures without lonely pairs (helices of length 1).

              (default=off)

              For  partition  function  folding  this  only  disallows  pairs that can only occur
              isolated. Other pairs may still occasionally occur as helices of length 1.

       --noGU Do not allow GU pairs.

              (default=off)

       --noClosingGU
              Do not allow GU pairs at the end of helices.

              (default=off)

       --nsp=STRING
              Allow other pairs in addition to the usual AU,GC,and GU pairs.

              Its argument is a comma separated list of additionally allowed pairs. If the  first
              character  is  a  "-"  then  AB  will  imply that AB and BA are allowed pairs, e.g.
              --nsp="-GA"  will allow GA and AG pairs. Nonstandard pairs  are  given  0  stacking
              energy.

       --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

       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

       Ivo L Hofacker, 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

       RNAcofold(l) RNAfold(l)