RNAdos - manual page for RNAdos 2.5.1
RNAdos [
OPTIONS]
RNAdos 2.5.1
Calculate the density of states for each energy band of an RNA
The program reads an RNA sequence and computes the density of states for each
energy band.
-
-h, --help
- Print help and exit
- --detailed-help
- Print help, including all details and hidden options, and
exit
-
-V, --version
- Print version and exit
- Command line options which alter the general behavior of
this program
-
-v, --verbose
- Be verbose.
- (default=off)
-
-s, --sequence=STRING
- The RNA sequence (ACGU)
-
-e, --max-energy=INT
- Structures are only counted until this threshold is
reached. Default is 0 kcal/mol.
- (default=`0')
-
-j, --numThreads=INT
- Set the number of threads used for calculations (only
available when compiled with OpenMP support)
-
-T, --temp=DOUBLE
- Rescale energy parameters to a temperature of temp C.
Default is 37C.
-
-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.
-
-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.
-
-b, --hashtable-bits=INT
- Set the size of the hash table for each cell in the
dp-matrices.
- (default=`20')
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
J. Cupal, I.L. Hofacker, P.F. Stadler (1996), "Dynamic programming
algorithm for the density of states of RNA secondary structures" Computer
Science and Biology 96, Proc. German Conf. on Bioinformatics 1996, pp.
184-186.
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
Gregor Entzian, Ronny Lorenz
If in doubt our program is right, nature is at fault. Comments should be sent to
[email protected].
RNAsubopt(1)