RNAaliduplex - manual page for RNAaliduplex 2.5.1
RNAaliduplex [
options]
<file1.aln> <file2.aln>
RNAaliduplex 2.5.1
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
-
-V, --version
- Print version and exit
- Below are command line options which alter the general
behavior of this program
-
-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
- print output sorted by free energy
- (default=off)
-
-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.
- --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. RNAfold -nsp
-GA will allow GA and AG pairs. Nonstandard pairs are given 0
stacking energy.
-
-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.
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
[email protected].
RNAduplex(1) RNAcofold(1) RNAfold(1)