NAME

       RNAPKplex - manual page for RNAPKplex 2.5.1

SYNOPSIS

       RNAPKplex [OPTION]...

DESCRIPTION

       RNAPKplex 2.5.1

       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.