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RNA2DFOLD(1)			 User Commands			  RNA2DFOLD(1)

       RNA2Dfold - manual page for RNA2Dfold 2.4.14

       RNA2Dfold [OPTIONS]...

       RNA2Dfold 2.4.14

       Compute	MFE  structure,	 partition  function and representative	sample
       structures of k,l neighborhoods

       The program  partitions	the  secondary	structure  space  into	(base-
       pair)distance  classes  according to two	fixed reference	structures. It
       expects a sequence and two secondary structures in dot-bracket notation
       as  its inputs. For each	distance class,	the MFE	representative,	Boltz-
       mann probabilities and Gibbs free energy	is computed.  Additionally,  a
       stochastic backtracking routine allows one to produce samples of	repre-
       sentative suboptimal secondary structures from each partition

       -h, --help
	      Print help and exit

	      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

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


       -j, --numThreads=INT
	      Set  the number of threads used for calculations (only available
	      when compiled with OpenMP	support)

       -p, --partfunc
	      calculate	partition function and thus,  Boltzmann	 probabilities
	      and Gibbs	free energy


	      backtrack	 a certain number of Boltzmann samples from the	appro-
	      priate k,l neighborhood(s)

	      backtrack	structures from	certain	k,l-neighborhood only, can  be
	      specified	multiple times (<k>:<l>,<m>:<n>,...)

       -S, --pfScale=DOUBLE
	      scaling factor for pf to avoid overflows

       --noBT do not backtrack structures, calculate energy contributions only


       -c, --circ
	      Assume a circular	(instead of linear) RNA	molecule.


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

       -K, --maxDist1=INT
	      maximum distance to first	reference structure

	      If this value is set all structures that exhibit a basepair dis-
	      tance greater than maxDist1 will be thrown into a	distance class
	      denoted by K=L=-1

       -L, --maxDist2=INT
	      maximum distance to second reference structure

	      If this value is set all structures that exhibit a basepair dis-
	      tance greater than maxDist1 will be thrown into a	distance class
	      denoted by K=L=-1

       -4, --noTetra
	      Do not include special tabulated stabilizing energies for	 tri-,
	      tetra- and hexaloop hairpins. Mostly for testing.


       -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 an input file.

       -d, --dangles=INT
	      How to treat "dangling end" energies for bases adjacent  to  he-
	      lices in free ends and multi-loops

	      (possible	values="0", "2"	default=`2')

	      With  -d2	dangling energies will be added	for the	bases adjacent
	      to a helix on both sides

	      in any case.

	      The option -d0 ignores dangling ends altogether (mostly for  de-

       --noGU Do not allow GU pairs


	      Do not allow GU pairs at the end of helices


       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

       R. Lorenz, C. Flamm, I.L. Hofacker (2009), "2D Projections of RNA fold-
       ing Landscapes",	GI, Lecture Notes in Informatics, German Conference on
       Bioinformatics 2009: 157, pp 11-20

       M. Zuker, P. Stiegler (1981), "Optimal computer folding	of  large  RNA
       sequences  using	 thermodynamic	and  auxiliary information", Nucl Acid
       Res: 9, pp 133-148

       J.S. McCaskill (1990), "The equilibrium	partition  function  and  base
       pair  binding probabilities for RNA secondary structures", Biopolymers:
       29, pp 1105-1119

       I.L. Hofacker and P.F. Stadler (2006), "Memory Efficient	Folding	 Algo-
       rithms for Circular RNA Secondary Structures", Bioinformatics

       D.  Adams  (1979),  "The	 hitchhiker's guide to the galaxy", Pan	Books,

       The calculation of mfe structures is based on dynamic programming algo-
       rithm  originally  developed by M. Zuker	and P. Stiegler. The partition
       function	algorithm is based on work by J.S. McCaskill.

       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

       Ronny Lorenz

       If  in doubt our	program	is right, nature is at fault.  Comments	should
       be sent to

RNA2Dfold 2.4.14		  August 2019			  RNA2DFOLD(1)


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