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RNAPDIST(1)			 User Commands			   RNAPDIST(1)

NAME
       RNApdist	- manual page for RNApdist 2.4.14

SYNOPSIS
       RNApdist	[OPTIONS]...

DESCRIPTION
       RNApdist	2.4.14

       Calculate  distances between thermodynamic RNA secondary	structures en-
       sembles

       This program reads RNA sequences	from stdin  and	 calculates  structure
       distances between the thermodynamic ensembles of	their secondary	struc-
       tures.

       To do this the partition	function and matrix of base pairing probabili-
       ties is computed	for each sequence. The probability matrix is then con-
       densed into a vector holding for	each base the probabilities  of	 being
       unpaired,  paired  upstream,  or	paired downstream, respectively. These
       profiles	are compared by	a standard alignment algorithm.

       The base	pair probabilities are also saved as  postscript  "dot	plots"
       (as  in	RNAfold) in the	files  "name_dp.ps", where name	is the name of
       the sequence, or	a number if unnamed.

       -h, --help
	      Print help and exit

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

       --full-help
	      Print help, including hidden options, and	exit

       -V, --version
	      Print version and	exit

   General Options:
       --noconv
	      Do not automatically substitude nucleotide "T" with "U"

	      (default=off)

   Algorithms:
       -X, --compare=p|m|f|c
	      Specify the comparison directive.	 (default=`p')

	      Possible arguments for this option are: -Xp compare  the	struc-
	      tures  pairwise  (p),  i.e.  first with 2nd, third with 4th etc.
	      -Xm calculate the	distance matrix	between	 all  structures.  The
	      output  is  formatted  as	 a lower triangle matrix.  -Xf compare
	      each structure to	the first one.	-Xc compare continuously, that
	      is i-th with (i+1)th structure.

       -B, --backtrack[=<filename>]
	      Print  an	 "alignment"  with  gaps  of the profiles. The aligned
	      structures are written to	<filename>, if specified.

	      (default=`none')

	      Within the profile output, the following symbols will be used:

       ()     essentially upstream (downstream)	paired bases

       {}     weakly upstream (downstream) paired bases

       |      strongly paired bases without preference

       ,      weakly paired bases without preference

       .      essentially unpaired bases.

	      If <filename> is not specified, the output is written to stdout,
	      unless the

	      "-Xm" option is set in which case	"backtrack.file" is used.

   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
	      set energy model for treatment of	dangling bases

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

       --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)

       -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.

       --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.

       -e, --energyModel=INT
	      Rarely used option to fold sequences from	the artificial ABCD...
	      alphabet,	where A	pairs B, C-D etc.  Use the  energy  parameters
	      for GC (-e 1) or AU (-e 2) pairs.

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

       S. Bonhoeffer, J.S. McCaskill, P.F. Stadler, P. Schuster	 (1993),  "RNA
       multi-structure landscapes", Euro Biophys J:22, pp 13-24

       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
       Peter F Stadler,	Ivo L Hofacker,	Sebastian Bonhoeffer.

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

RNApdist 2.4.14			  August 2019			   RNAPDIST(1)

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

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