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.