NAME

     RNAEVAL - calculate energy of RNA sequences on given  secon-
     dary structure

SYNOPSIS

     RNAeval [-T temp] [-4] [-d[0|1|2|3]] [-logML] [-e  1|2]  [-P
     paramfile]

DESCRIPTION

     RNAeval evaluates the free energy  of  an  RNA  molecule  in
     fixed secondary structure. Sequences and structures are read
     alternately from stdin. The energy in Kcal/Mol is written to
     stdout.
     The program will continue to read new sequences  and  struc-
     tures  until  a line consisting of the single character @ or
     an end of file condition is encountered.

OPTIONS

     -d   Do not give  stabilizing  energies  to  unpaired  bases
          adjacent  to helices in multiloops and free ends ("dan-
          gling  ends").  Same  as  -d0,  opposite  of  -d1  (the
          default).

     -d2  Treat dangling ends as in the partition function  algo-
          rithm, i.e. bases adjacent to helices in multiloops and
          free  ends  give  a  stabilizing  energy  contribution,
          regardless whether they're paired or unpaired.

     -d3  Allow coaxial stacking of adjacent  helices  in  multi-
          loops.

     -logML
          Let multiloop energies depend  logarithmically  on  the
          size, instead of the usual linear energy function.

     The -T, -4, -e, -P, options work as in RNAfold.

REFERENCES

     If you use this program in your work you might want to 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

VERSION

     This man page documents version 1.4 Vienna RNA Package

AUTHOR

     Ivo L Hofacker and Peter F Stadler.

BUGS

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