NAME

       RNAPKplex - manual page for RNAPKplex 2.4.17

SYNOPSIS

       RNAPKplex [OPTION]...

DESCRIPTION

       RNAPKplex 2.4.17

       predicts RNA secondary structures including pseudoknots

       Computes  RNA  secondary  structures by first making two sequence intervals accessible and unpaired using
       the algorithm of RNAplfold and then calculating the energy of the interaction of those two intervals. The
       algorithm uses O(n^2*w^4) CPU time and O(n*w^2) memory space.  The algorithm furthermore always considers
       dangle=2 model.

       It  also  produces a PostScript file with a plot of the pseudoknot-free  secondary  structure  graph,  in
       which the bases  forming  the  pseuodknot are marked red.

       Sequences  are read in a simple text format where each sequence occupies a single line. Each sequence may
       be preceded by a line of the form
       > name
       to assign a name to the sequence. If a name is given in the input, the
        PostScript file "name.ps" is produced for the structure graph.  Other- wise  the  file  name defaults to
       PKplex.ps.  Existing  files  of  the same name will be overwritten.  The input format is similar to fasta
       except that  even  long  sequences may  not  be  interrupted  by  line  breaks,  and   the  header  lines
       are  optional.   The program will continue to read new sequences until a line consisting  of  the  single
       character @ or an end of file condition is encountered.

       -h, --help
              Print help and exit

       --detailed-help
              Print help, including all details and hidden options, and exit

       -V, --version
              Print version and exit

       -c, --cutoff=FLOAT
              Report only base pairs with an average probability > cutoff in the dot plot

              (default=`0.01')

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

       -4, --noTetra
              Do not include special stabilizing energies for certain tetra-loops. Mostly for testing.

              (default=off)

       --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)

       --noconv
              Do not automatically substitude nucleotide "T" with "U"

              (default=off)

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

              (default=`empty')

              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.

       -e, --energyCutoff=DOUBLE
              Energy  cutoff or pseudoknot initiation cost.  Minimum energy gain of a pseudoknot interaction for
              it to be returned. Pseudoknots with smaller energy gains are rejected.

              (default=`-8.10')

       -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.

       -v, --verbose
              print verbose output

              (default=off)

       -s, --subopts=DOUBLE
              print suboptimal structures whose energy difference of the pseudoknot to the optimum pseudoknot is
              smaller than the given value.

              (default=`0.0')

              NOTE:  The  final  energy  of  a  structure is calculated as the sum of the pseudoknot interaction
              energy, the penalty for initiating a  pseudoknot and the energy of the pseudoknot-free part of the
              structure.  The  -s option only takes the pseudoknot interaction energy into account, so the final
              energy differences may be bigger than the specified value (default=0.).

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

       Wolfgang Beyer

REPORTING BUGS

       If in doubt our program is right, nature is at fault.  Comments should be sent to rna@tbi.univie.ac.at.