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RNAPKPLEX(1)			 User Commands			  RNAPKPLEX(1)

NAME
       RNAPKplex - manual page for RNAPKplex 2.4.14

SYNOPSIS
       RNAPKplex [OPTIONS]...

DESCRIPTION
       RNAPKplex 2.4.14

       predicts	RNA secondary structures including pseudoknots

       Computes	 RNA  secondary	structures by first making two sequence	inter-
       vals 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  al-
       gorithm 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  charac-
       ter @ 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  oc-
	      cur 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. Pseudo-
	      knots with smaller energy	gains are rejected.

	      (default=`-8.10')

       -P, --paramFile=paramfile
	      Read energy parameters from paramfile, instead of	using the  de-
	      fault parameter set.

	      Different	 sets  of energy parameters for	RNA and	DNA should ac-
	      company your distribution.  See the RNAlib documentation for de-
	      tails 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 pseu-
	      doknot 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 big-
	      ger 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	Struc-
       tures", 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  modifica-
       tion 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.

RNAPKplex 2.4.14		  August 2019			  RNAPKPLEX(1)

NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS

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