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 immediately. 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  structure can not be found.  If no value is supplied with this option,
              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 structure 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 helices in free ends and
              multi-loops

              (default=`2')

              With -d1 only unpaired bases can participate in at most one dangling 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 interior 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 using 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 default parameter set.

              Different  sets  of  energy  parameters  for  RNA  and  DNA  should  accompany your
              distribution.  See the RNAlib documentation for details 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 Structures", 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 prediction", 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  modification  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 interrupted 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.