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RNAINVERSE - find RNA sequences with given secondary structure
RNAinverse [-F[mp]] [-R repeats]] [-v] [-a
alphabet] [-f final] [-T
temp] [-d[0|1|2|3] [-4] [-noGU] [-noCloseGU]
[-P paramfile] [-e 1|2] [-nsp
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 specified 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 structure. 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 distance 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
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.
- 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
- -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 target structure can not be
- in conjunction with -R and a negative repeats,
print the last subsequence and substructure for each unsuccessful
- -a alphabet
- Find sequences using only bases from alphabet.
The -T, -d, -4, -noGU,
-noCloseGU, -e, -P, -nsp, options work
as in RNAfold
To search 5 times for sequences forming a simple hairpin structure
interrupted by one GA mismatch call
RNAinverse -R 5
and enter the lines
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
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 information, Nucl Acid
Res 9: 133-148
J.S. McCaskill (1990) The equilibrium partition function and base
pair binding probabilities for RNA secondary structures,
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,
This man page documents version 1.8.5 Vienna RNA Package.
Ivo L Hofacker.
If in doubt our program is right, nature is at fault. Comments
should be sent to firstname.lastname@example.org.
This document was created by man2html,
using the manual pages.
Time: 07:19:16 GMT, February 23, 2011