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RNAEVAL - calculate energy of RNA sequences on given secondary
RNAeval [-T temp] [-4] [-d[0|1|2|3]] [-logML] [-e
1|2] [-P paramfile] [-circ] [-v]
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
The program will continue to read new sequences and structures
until a line consisting of the single character "@" or an end of
file condition is encountered.
If the input sequence or structure contains the separator character
"&" the program calculates the energy of the co-folding of two
RNA strands, where the "&" marks the boundary between the two
- Do not give stabilizing energies to unpaired bases adjacent
to helices in multiloops and free ends ("dangling ends"). Same as
-d0, opposite of -d1 (the default).
- Treat dangling ends as in the partition function algorithm,
i.e. bases adjacent to helices in multiloops and free ends give a
stabilizing energy contribution, regardless whether they're paired
- Allow coaxial stacking of adjacent helices in
- Let multiloop energies depend logarithmically on the size,
instead of the usual linear energy function.
- Assume a cricular (rather than linear) RNA
- Print out energy contribution of each loop in the
The -T, -4, -e, -P, options work as
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
This man page documents version 1.8.5 Vienna RNA Package
Ivo L Hofacker and Peter F Stadler.
If in doubt our program is right, nature is at fault. Comments
should be sent to email@example.com.
This document was created by man2html,
using the manual pages.
Time: 07:19:16 GMT, February 23, 2011