Ubuntu Manpage: RNAdos - manual page for RNAdos 2.7.0

Provided by: vienna-rna_2.7.0+dfsg-1_amd64

NAME

       RNAdos - manual page for RNAdos 2.7.0

SYNOPSIS

       RNAdos [OPTIONS]

DESCRIPTION

RNAdos 2.7.0

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

--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.

I/O Options:
Command line options for input and output (pre-)processing

-s, --sequence=STRING
The RNA sequence (ACGU).

-j, --numThreads=INT
Set the number of threads used for calculations (only available when compiled with OpenMP support)

--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=`RNAdos.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. The Minimum free
energy (MFE) and a structure representative are calculated in any case.

-e, --max-energy=INT
Structures are only counted until this threshold is reached. Default is 0 kcal/mol.

(default=`0')

-b, --hashtable-bits=INT
Set the size of the hash table for each cell in the dp-matrices.

(default=`20')

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.

--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.

--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.

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

       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

AUTHOR

       Gregor Entzian, Ronny Lorenz

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