NAME

       RNAduplex - manual page for RNAduplex 2.4.17

SYNOPSIS

       RNAduplex [OPTION]...

DESCRIPTION

       RNAduplex 2.4.17

       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

   General Options:
              Below are command line options which alter the general behavior of this program

       -s, --sorted
              sort the printed output by free energy

              (default=off)

       --noconv
              Do not automatically substitude 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.

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

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

              (default=off)

       -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)

       -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.

       --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. RNAfold -nsp -GA  will allow GA and
              AG pairs. Nonstandard pairs are given 0 stacking energy.

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)

RNAduplex 2.4.17                                  January 2022                                      RNADUPLEX(1)