NAME

     RNAINVERSE - find RNA sequences with given secondary  struc-
     ture

SYNOPSIS

     RNAinverse [-F[mp]] [-R repeats]] [-v] [-a  [-f  final]  [-T
     temp] [-d[0|1|2|3] [-4] [-P paramfile] [-e 1|2] [-nsp pairs]

DESCRIPTION

     RNAinverse 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 speci-
     fied  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  struc-
     ture.  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 dis-
     tance  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 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.

OPTIONS

     -F[mp]
          Use minimum energy (-Fm),  partition  function  folding
          (-Fp)  or  both (-Fmp). 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. The default is -Fm.

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

     -R repeats
          Search repeatedly for the same structure. 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 tar-
          get structure can not be found.

     -v   in conjunction with -R and a  negative  repeats,  print
          the  last  subsequence and substructure for each unsuc-
          cessful search.

     -a alphabet
          Find sequences using only bases from alphabet.

     The -T, -d, -4, -noGU, -noCloseGU,  -e,  -P,  -nsp,  options
     work as in RNAfold

EXAMPLE

     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

REFERENCES

     The calculation of minimum free energy structures  is  based
     on  dynamic programming algorithm originally developed by M.
     Zuker and P. Stiegler.  The partition function algorithm  is
     based on work by J.S. McCaskill.
     If this Program proves useful for your work please cite:

     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:
     167-188
     Other useful references are:
     M. Zuker, P. Stiegler (1981)  Optimal  computer  folding  of
     large RNA sequences using thermodynamic and auxiliary infor-
     mation, Nucl Acid Res 9: 133-148
     J.S. McCaskill (1990) The equilibrium partition function and
     base  pair  binding  probabilities  for RNA secondary struc-
     tures, Biopolymers 29: 1105-1119
     D.H. Turner N. Sugimoto and S.M. Freier (1988) RNA structure
     prediction, Ann Rev Biophys Biophys Chem 17: 167-192
     D. Adams (1979) The hitchhiker's guide to  the  galaxy,  Pan
     Books, London

VERSION

     This man page documents version 1.4 Vienna RNA Package.

AUTHOR

     Ivo L Hofacker.

BUGS

     If in doubt our program is right, nature is at fault.   Com-
     ments should be sent to ivo@tbi.univie.ac.at.