NAME

       RNAaliduplex - manual page for RNAaliduplex 2.5.1

SYNOPSIS

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

DESCRIPTION

       RNAaliduplex 2.5.1

       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

       -V, --version
              Print version and exit

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

       -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
              print output sorted by free energy

              (default=off)

   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)

       --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.

       -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.

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)

RNAaliduplex 2.5.1                                 April 2024                                    RNAALIDUPLEX(1)