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RNAINVERSE(1)			 User Commands			 RNAINVERSE(1)

NAME
       RNAinverse - manual page	for RNAinverse 2.4.17

SYNOPSIS
       RNAinverse [OPTION]...

DESCRIPTION
       RNAinverse 2.4.17

       Find RNA	sequences with given secondary structure

       The program searches for	sequences folding into a predefined structure,
       thereby inverting the folding algorithm.	Target structures (in  bracket
       notation)  and  starting	 sequences for the search are read alternately
       from stdin.  Characters in the start sequence other than	"AUGC" (or the
       alphabet	 specified with	-a) will be treated as wild cards and replaced
       by a random character. Any lower	case characters	in the start  sequence
       will  be	 kept fixed during the search. If necessary, the sequence will
       be elongated to the length of the structure. Thus a string of  "N"s  as
       well  as	a blank	line specify a random start sequence.  For each	search
       the best	sequence found and its Hamming distance	to the start  sequence
       are  printed to stdout. If the the search was unsuccessful, a structure
       distance	to the target is appended.  The	-Fp and	-R options can	modify
       the  output  format,  see  commandline options below.  The program will
       continue	to read	new structures and 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

       --full-help
	      Print help, including 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

       -R, --repeat[=INT]
	      Search repeatedly	for the	same structure.	  If  an  argument  is
	      supplied	to  this option	it must	follow the option flag immedi-
	      ately. E.g.: -R5

	      (default=`100')

	      If repeats is negative search until  --repeats  exact  solutions
	      are  found,  no  output  is  done	 for unsuccessful searches. Be
	      aware, that the program will not terminate if the	target	struc-
	      ture  can	 not  be found.	 If no value is	supplied with this op-
	      tion, the	default	value is used.

       -a, --alphabet=ALPHABET
	      Find sequences using only	nucleotides from a given alphabet.

       -v, --verbose
	      In conjunction with a negative value supplied to -R,  print  the
	      last subsequence and substructure	for each unsuccessful search.

	      (default=off)

   Algorithms:
	      Select  additional  algorithms  which  should be included	in the
	      calculations.

       -F, --function=mp
	      Use minimum energy (-Fm),	partition function  folding  (-Fp)  or
	      both (-Fmp).

	      (default=`m')

	      In partition function mode, the probability of the target	struc-
	      ture exp(-E(S)/kT)/Q is maximized. This probability  is  written
	      in  brackets  after  the found sequence and Hamming distance. In
	      most cases you'll	want to	use the	-f option in conjunction  with
	      -Fp, see below.

       -f, --final=FLOAT
	      In  combination with -Fp stop search when	sequence is found with
	      E(s)-F is	smaller	than final, where F=-kT*ln(Q).

   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
	      How to treat "dangling end" energies for bases adjacent  to  he-
	      lices in free ends and multi-loops

	      (default=`2')

	      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.

       --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

       D.H. Turner, N. Sugimoto, S.M. Freier (1988),  "RNA  structure  predic-
       tion", Ann Rev Biophys Biophys Chem: 17,	pp 167-192

       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

       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

EXAMPLES
       To search 5 times for sequences forming a simple	hairpin	structure  in-
       terrupted by one	GA mismatch call

	 $ RNAinverse -R 5

       and enter the lines

	 (((.(((....))).)))
	 NNNgNNNNNNNNNNaNNN

AUTHOR
       Ivo L Hofacker

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

RNAinverse 2.4.17		 November 2020			 RNAINVERSE(1)

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

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