RNAinverse

RNAinverse - manual page for RNAinverse 2.7.2

Synopsis

RNAinverse [OPTION]...

DESCRIPTION

RNAinverse 2.7.2

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.

-v, --verbose

In conjunction with a negative value supplied to -R, print the last subsequence and substructure for each unsuccessful search.

(default=off)

Lower the log level setting such that even INFO messages are passed through.

--log-level=level

Set log level threshold. (default=”2”)

By default, any log messages are filtered such that only warnings (level 2) or errors (level 3) are printed. This setting allows for specifying the log level threshold, where higher values result in fewer information. Log-level 5 turns off all messages, even errors and other critical information.

--log-file[=filename]

Print log messages to a file instead of stderr. (default=”RNAinverse.log”)

--log-time

Include time stamp in log messages.

(default=off)

--log-call

Include file and line of log calling function.

(default=off)

Algorithms:

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 :option:-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).

-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=”1”)

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.

--init-strategy=strategy

Use a specific strategy to generate an initial sequence seed.

(default=”random”)

This option allows for changing the initial sequence seed generator strategy in cases where no start sequence is specified. By default, the sequence characters are randomly chosen with equal probabilities for any nucleotide. A more elaborate method is the “LinearBP” approach (Boury et al. 2025) to find a good starting sequence candidate that already fulfills optimality within a base pair model. Note, that currently this option has no effect if a start sequence is provided as an input. Available strategies are:

“random”: Generate a random sequence with equal nucleotide probabilities.

“linearbp”: Use the “LinearBP” approach.

-a, --alphabet=ALPHABET

Find sequences using only nucleotides from a given alphabet.

Energy Parameters:

Energy parameter sets can be adapted or loaded from user-provided input files

-T, --temp=DOUBLE

Rescale energy parameters to a temperature of temp C. Default is 37C.

(default=”37.0”)

-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.

-4, --noTetra

Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins.

(default=off)

Mostly for testing.

--salt=DOUBLE

Set salt concentration in molar (M). Default is 1.021M.

Model Details:

Tweak the energy model and pairing rules additionally using the following parameters

-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 enclosed 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)

--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.

--energyModel=INT

Set energy model.

Rarely used option to fold sequences from the artificial ABCD… alphabet, where A pairs B, C-D etc. Use the energy parameters for GC (--energyModel 1) or AU (--energyModel 2) pairs.

--helical-rise=FLOAT

Set the helical rise of the helix in units of Angstrom.

(default=”2.8”)

Use with caution! This value will be re-set automatically to 3.4 in case DNA parameters are loaded via -P DNA and no further value is provided.

--backbone-length=FLOAT

Set the average backbone length for looped regions in units of Angstrom.

(default=”6.0”)

Use with caution! This value will be re-set automatically to 6.76 in case DNA parameters are loaded via -P DNA and no further value is provided.

-h, --help

display help and exit

--full-help

display help, including hidden options, and exit

--detailed-help

display help, including all details and hidden options, and exit

-V, --version

output version and exit

REFERENCES

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

T. Boury, S. Gardelle, L. Bulteau, Y. Ponty (2025), “RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs”, Algorithms Mol Biol: 20(1):20

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

EXAMPLES

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

AUTHOR

Ivo L Hofacker

REPORTING BUGS

If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.