NAME

       RNAaliduplex - manual page for RNAaliduplex 2.6.4

SYNOPSIS

       RNAaliduplex [options] <file1.aln> <file2.aln>

DESCRIPTION

       RNAaliduplex 2.6.4

       Predict conserved RNA-RNA interactions between two alignments

       The  program  reads two alignments of RNA sequences in CLUSTAL format and predicts optimal
       and suboptimal binding sites, hybridization energies and the corresponding structures. The
       calculation  takes  only inter-molecular base pairs into account, for the general case use
       RNAcofold. The  use  of  alignments  allows  one  to  focus  on  binding  sites  that  are
       evolutionary  conserved.  Note, that the two input alignments need to have equal number of
       sequences and the same order, i.e. the 1st sequence in file1 will be hybridized to the 1st
       in file2 etc.

       The  computed binding sites, energies, and structures 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

   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.

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

              (default=off)

   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

       RNAduplex(1) RNAcofold(1) RNAfold(1)