NAME

     RNAsubopt - calculate  suboptimal  secondary  structures  of
     RNAs

SYNOPSIS

     RNAsubopt [-e range] [-ep prange]  [-s]  [-lodos]  [-T temp]
     [-d[0|1|2|3]]   [-4]   [-noGU]  [-noCloseGU]  [-P paramfile]
     [-logML] [-nsp pairs]

DESCRIPTION

     RNAsubopt reads RNA sequences from stdin and calculates  all
     suboptimal secondary structures within a user defined energy
     range above the minimum free energy  (mfe).  It  prints  the
     suboptimal  structures  in  bracket notation followed by the
     energy in kcal/mol to  stdout.   The  number  of  structures
     returned  typically  grows  exponentially with both sequence
     length and energy range.

OPTIONS

     -e range  Calculate  suboptimal  structures   within   range
     kcal/mol of the mfe. Default is 1.

     -s   Sort the structures by energy. Uses more memory and CPU
          time.  For  larger calculations, better pipe the output
          through `sort +1n'.

     -lodos
          Calculate the Lower Density  of  States.  Output  lines
          consist  of  an energy followed by the number of struc-
          tures with that energy, suitable for plotting the  den-
          sity  of  states.  Does  not print the structures them-
          selves.

     -d[0|1|2|3]
          Change treatment of dangling ends, as  in  RNAfold  and
          RNAeval.   The default is -d2 (as in partition function
          folding). If -d1 or -d3 are specified energies are  re-
          evaluated  before  printing,  which may incur a perfor-
          mance penalty (see also -ep and -logML).

     -logML
          re-calculate energies of structures using a logarithmic
          energy  function  for multi-loops. This option does not
          effect structure generation, only the energies that  is
          printed out. Since logML lowers energies somewhat, some
          structures may be missing.

     -ep prange
          Only print structures with energy within prange of  the
          mfe. Useful in conjunction with -logML, -d1 or -d3.

     -noLP
          Only produce structures without lonely  pairs  (helices
          of  length  1).  This  reduces the number of structures
          drastically and should therefore  be  used  for  longer
          sequences and larger energy ranges.

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

     Please cite:
     S. Wuchty, W. Fontana, I. L. Hofacker and P. Schuster  "Com-
     plete  Suboptimal Folding of RNA and the Stability of Secon-
     dary Structures", Biopolymers, 49, 145-165 (1999)

AUTHORS

     Stefan Wuchty, Ivo L Hofacker, Walter Fontana.