RNAinverse - manual page for RNAinverse 2.5.1
RNAinverse [
OPTION]...
RNAinverse 2.5.1
Find RNA sequences with given secondary structure
The program 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 commandline
options below. 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.
-
-h, --help
- Print help and exit
- --detailed-help
- Print help, including all details and hidden options, and
exit
- --full-help
- Print help, including hidden options, and exit
-
-V, --version
- Print version and exit
- Below are command line options which alter the general
behavior of this program
-
-R, --repeat[=INT]
- Search repeatedly for the same structure. If an argument is
supplied to this option it must follow the option flag immediately. E.g.:
-R5
- (default=`100')
- 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 found. If no value is supplied with this option, the default value is
used.
-
-a, --alphabet=ALPHABET
- Find sequences using only nucleotides from a given
alphabet.
-
-v, --verbose
- In conjunction with a negative value supplied to -R,
print the last subsequence and substructure for each unsuccessful
search.
- (default=off)
- Select additional algorithms which should be included in
the calculations.
-
-F, --function=mp
- Use minimum energy (-Fm), partition function folding
( -Fp) or both (-Fmp).
- (default=`m')
- 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.
-
-f, --final=FLOAT
- In combination with -Fp stop search when sequence is
found with E(s)-F is smaller than final, where F=-kT*ln(Q).
-
-T, --temp=DOUBLE
- Rescale energy parameters to a temperature of temp C.
Default is 37C.
-
-4, --noTetra
- Do not include special tabulated stabilizing energies for
tri-, tetra- and hexaloop hairpins. Mostly for testing.
- (default=off)
-
-d, --dangles=INT
- How to treat "dangling end" energies for bases
adjacent to helices in free ends and multi-loops
- (default=`2')
- With -d1 only unpaired bases can participate in at
most one dangling end. With -d2 this check is ignored, dangling
energies will be added for the bases adjacent to a helix on both sides in
any case; this is the default for mfe and partition function folding (
-p). The option -d0 ignores dangling ends altogether (mostly
for debugging). With -d3 mfe folding will allow coaxial stacking of
adjacent helices in multi-loops. At the moment the implementation will not
allow coaxial stacking of the two interior pairs in a loop of degree 3 and
works only for mfe folding.
- Note that with -d1 and -d3 only the MFE
computations will be using this setting while partition function uses
-d2 setting, i.e. dangling ends will be treated differently.
- --noGU
- Do not allow GU pairs
- (default=off)
- --noClosingGU
- Do not allow GU pairs at the end of helices
- (default=off)
-
-P, --paramFile=paramfile
- Read energy parameters from paramfile, instead of using the
default parameter set.
- Different sets of energy parameters for RNA and DNA should
accompany your distribution. See the RNAlib documentation for details on
the file format. When passing the placeholder file name "DNA",
DNA parameters are loaded without the need to actually specify any input
file.
-
--nsp=STRING
- Allow other pairs in addition to the usual AU,GC,and GU
pairs.
- Its argument is a comma separated list of additionally
allowed pairs. If the first character is a "-" then AB will
imply that AB and BA are allowed pairs. e.g. RNAfold -nsp
-GA will allow GA and AG pairs. Nonstandard pairs are given 0
stacking energy.
-
-e, --energyModel=INT
- Rarely used option to fold sequences from the artificial
ABCD... alphabet, where A pairs B, C-D etc. Use the energy parameters for
GC ( -e 1) or AU ( -e 2) pairs.
If you use this program in your work you might want to cite:
R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F.
Stadler and I.L. Hofacker (2011), "ViennaRNA Package 2.0",
Algorithms for Molecular Biology: 6:26
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, pp 167-188
R. Lorenz, I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and
soft constraints", Algorithms for Molecular Biology 11:1 pp 1-13
D.H. Turner, N. Sugimoto, S.M. Freier (1988), "RNA structure
prediction", Ann Rev Biophys Biophys Chem: 17, pp 167-192
M. Zuker, P. Stiegler (1981), "Optimal computer folding of large RNA
sequences using thermodynamic and auxiliary information", Nucl Acid Res:
9, pp 133-148
J.S. McCaskill (1990), "The equilibrium partition function and base pair
binding probabilities for RNA secondary structures", Biopolymers: 29, pp
1105-1119
The energy parameters are taken from:
D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M.
Zuker, D.H. Turner (2004), "Incorporating chemical modification
constraints into a dynamic programming algorithm for prediction of RNA
secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292
D.H Turner, D.H. Mathews (2009), "NNDB: The nearest neighbor parameter
database for predicting stability of nucleic acid secondary structure",
Nucleic Acids Research: 38, pp 280-282
To search 5 times for sequences forming a simple hairpin structure interrupted
by one GA mismatch call
$ RNAinverse -R 5
and enter the lines
(((.(((....))).)))
NNNgNNNNNNNNNNaNNN
Ivo L Hofacker
If in doubt our program is right, nature is at fault. Comments should be sent to
[email protected].