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RNAALIDUPLEX(1)			 User Commands		       RNAALIDUPLEX(1)

       RNAaliduplex - manual page for RNAaliduplex 2.4.14

       RNAaliduplex [options] _file1.aln_ _file2.aln_

       RNAaliduplex 2.4.14

       Predict conserved RNA-RNA interactions between two alignments

       The program reads two alignments	of RNA sequences in CLUSTAL format and
       predicts	optimal	and suboptimal binding sites,  hybridization  energies
       and  the	corresponding structures. The calculation takes	only inter-mo-
       lecular base pairs into account,	for the	general	 case  use  RNAcofold.
       The  use	 of  alignments	 allows	one to focus on	binding	sites that are
       evolutionary conserved. Note, that the two  input  alignments  need  to
       have  equal  number  of	sequences and the same order, i.e. the 1st se-
       quence in file1 will be hybridized to the 1st in	file2 etc.

       The computed binding sites, energies, and  structures  are  written  to
       stdout,	one structure per line.	Each line consist of: The structure in
       dot bracket format with a "&" separating	the two	strands. The range  of
       the  structure in the two sequences in the format  "from,to : from,to";
       the energy of duplex structure in kcal/mol.  The	format	is  especially
       useful  for  computing  the  hybrid structure between a small probe se-
       quence and a long target	sequence.

       -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

       -e, --deltaEnergy=range
	      Compute  suboptimal structures with energy in a certain range of
	      the optimum (kcal/mol). Default is calculation of	mfe  structure

       -s, --sorted
	      print output sorted by free energy


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

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


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


	      With -d1 only unpaired bases can participate in at most one dan-
	      gling  end.   With  -d2 this check is ignored, dangling energies
	      will be added for	the bases adjacent to a	helix on both sides in
	      any  case;  this	is  the	default	for mfe	and partition function
	      folding (-p).  The option	-d0 ignores dangling  ends  altogether
	      (mostly for debugging).  With -d3	mfe folding will allow coaxial
	      stacking of adjacent helices in multi-loops. At the  moment  the
	      implementation  will not allow coaxial stacking of the two inte-
	      rior pairs in a loop of degree 3 and works only for mfe folding.

	      Note that	with -d1 and -d3 only the MFE computations will	be us-
	      ing this setting while partition function	uses -d2 setting, i.e.
	      dangling ends will be treated differently.

       --noLP Produce structures without lonely	pairs (helices of length 1).


	      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


	      Do not allow GU pairs at the end of helices


	      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.

       -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.

       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

       Ivo L Hofacker, Ronny Lorenz

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

       RNAduplex(1) RNAcofold(1) RNAfold(1)

RNAaliduplex 2.4.14		  August 2019		       RNAALIDUPLEX(1)


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