RNAaliduplex - manual page for RNAaliduplex 2.6.4
RNAaliduplex [options] <file1.aln>
<file2.aln>
RNAaliduplex 2.6.4
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
- 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 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).
- 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 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.
- --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.
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
Ivo L Hofacker, Ronny Lorenz
If in doubt our program is right, nature is at fault. Comments
should be sent to rna@tbi.univie.ac.at.
RNAduplex(1) RNAcofold(1) RNAfold(1)