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RNAsubopt - calculate suboptimal secondary structures of RNAs
RNAsubopt [-e range] [-ep prange] [-s]
[-p n] [-T temp] [-d[0|1|2|3]] [-4] [-noGU]
[-noCloseGU] [-P paramfile] [-logML] [-nsp pairs] [-circ]
RNAsubopt reads RNA sequences from stdin and (in the default
-e mode) 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. Be careful, the number of
structures returned grows exponentially with both sequence length
and energy range.
Alternatively, when used with the -p option, RNAsubopt produces
Boltzmann weighted samples of secondary structures.
Sequences are read in the usual format, i.e. each sequence
occupies a single line, possibly preceded by a fasta-style header
line of the form
- -e range
- Calculate suboptimal structures within range kcal/mol of
the mfe. Default is 1.
- Sort the structures by energy. Since the sort in is done in
memory, this becomes impractical when the number of structures
produced goes into millions. In such cases better pipe the output
through `sort +1n'.
- -p n
- Instead of producing all suboptimals in an energy range,
produce a random sample of n suboptimal structures, drawn
with probabilities equal to their Boltzmann weights via stochastic
backtracking in the partition function. The -e and -p options a
- 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 the structures are generated as with -d2 but
energies are re-evaluated before printing.
- re-calculate energies of structures using a logarithmic energy
function for multi-loops before output. This option does not effect
structure generation, only the energies that is printed out. Since
logML lowers energies somewhat, some structures may be
- -ep prange
- Only print structures with energy within prange of the
mfe. Useful in conjunction with -logML, -d1 or -d3: while the -e
option specifies the range before energies are re-evaluated, -ep
specifies the maximum energy after re-evaluation.
- 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
- Assume a circular (instead of linear) RNA molecule.
The -T, -4, -noGU, -noCloseGU,
-P, -nsp, options work as in RNAfold.
S. Wuchty, W. Fontana, I. L. Hofacker and P. Schuster "Complete
Suboptimal Folding of RNA and the Stability of Secondary
Structures", Biopolymers, 49, 145-165 (1999)
This man page documents version 1.8.5 Vienna RNA Package.
Ivo L Hofacker, Stefan Wuchty, Walter Fontana.
Send comments and bug reports to <email@example.com>
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Time: 07:19:16 GMT, February 23, 2011