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.