# RNAaliduplex

RNAaliduplex - manual page for RNAaliduplex 2.7.0

## Synopsis

    RNAaliduplex [options] <file1.aln> <file2.aln>

## DESCRIPTION

RNAaliduplex 2.7.0

Predict conserved RNA-RNA interactions between two alignments

The program reads two alignments of RNA sequences in CLUSTAL format and predicts optimal and suboptimal binding sites, hybridization energies and the corresponding structures. The calculation takes only inter-molecular base pairs into account, for the general case use RNAcofold. The use of alignments allows one to focus on binding sites that are evolutionary conserved. Note, that the two input alignments need to have equal number of sequences and the same order, i.e. the 1st sequence in file1 will be hybridized to the 1st in file2 etc.

The computed binding sites, energies, and structures are written to stdout, one structure per line. Each line consist of: The structure in dot bracket format with a “&” separating the two strands. The range of the structure in the two sequences in the format “from,to : from,to”; the energy of duplex structure in kcal/mol. The format is especially useful for computing the hybrid structure between a small probe sequence and a long target sequence.

-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

-v, --verbose

  Be verbose. (default=off)

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

### Algorithms:

> Select additional algorithms which should be included in the calculations.

-e, --deltaEnergy=range

  Compute suboptimal structures with energy in a certain range of the optimum (kcal/mol). Default is calculation of mfe structure only.

-s, --sorted

  Sort output by free energy.

  (default=off)

### 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. The placeholder file name `DNA` can be used to load DNA parameters 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.

--saltInit=DOUBLE

  Provide salt correction for duplex initialization (in kcal/mol).

### 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.

--noLP

  Produce structures without lonely pairs (helices of length 1).

  (default=off)

  For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1.

--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. `--nsp=`”-GA” will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.

--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.

--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=”RNAaliduplex.log”)

--log-time

  Include time stamp in log messages.

  (default=off)

--log-call

  Include file and line of log calling function.

  (default=off)

## 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

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

## AUTHOR

Ivo L Hofacker, Ronny Lorenz

## REPORTING BUGS

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

## SEE ALSO

RNAduplex(1) RNAcofold(1) RNAfold(1)