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antaRNA - Variables

Command Line Variables to antaRNA


-h, --help
Promts some basic help text.

Mandatory Variables

-Cstr CSTR, --Cstr CSTR
Structure constraint using RNA dotbracket notation with fuzzy block constraint.
Fuzzy Capital Case Constraint does not enforce any structure. Fuzzy Lower Case Constraint checks for at least one abse pair present in a respective block.

Objective target GC content in [0,1]. This constraint can be extended to GC distributions.This can be done by using -tGCmax or -tGCvar options. See there.
The tGC variable can be used multiple times, so that different ares of target GC can be achieved. This should be done in the format e.g. --tGC 0.4:1-4 --tGC 0.5 5-10 . If multiple target GC are defined, no definition gaps are allowed.

Optional Variables

Constraint Variables

-Cseq CSEQ, --Cseq CSEQ
Sequence constraint using RNA nucleotide alphabet {A,C,G,U} and wild-card "N".
Capital letters enforce hard constraint and lead to terrain pruning. Lower characters of A,C,G and U allow soft constraining.
Constraint Type: String

-l LEVEL, --level LEVEL
Sets the level of allowed influence of sequence constraint on the structure constraint
[0:no influence; 1: ACGU; 2: RYSWKM; 3: BDHV].
A higher level always includes the inducing characters of all lower levels.
Constraint Type: int

Provides a maximum tGC value [0,1] for the case of uniform distribution sampling. The regular tGC value serves as minimum value.
Default Value: -1.0, TYPE: float

Provides a tGC variance (sigma square) for the case of normal distribution sampling. The regular tGC value serves as expectation value (mu).
Default Value: -1.0, TYPE: float

-p, --pseudoknots
Switch to pseudoknot based prediction using pKiss. Check the pseudoknot parameter usage with the -pkPar variable!!!

-pkPar, --pseudoknot_parameters
Enable optimized parameters for the usage of pseudo knots (Further parameter input will be ignored).

--strategy STRATEGY
Defining the pKiss folding strategy.
Default Value: A, TYPE: String

-GU, --useGUBasePair
Allowing GU base pairs.

-noLP, --noLPmanagement
Disallowing antaRNA LP-management during the folding and the subsequent evaluative function.

Provides a temperature for the folding algorithms.
Default Value: 37.0, TYPE: Float

Changes the energy parameterfile of RNAfold. If using this explicitly, please provide a suitable energy file delivered by RNAfold.
Default Value: , TYPE: String

Output Modifier Variables

Number of sequences which shall be produced during the execution of a call of the program.
Constraint Type: Integer

-s SEED, --seed SEED
Provides a seed value for the used pseudo random number generator.
Default Value: "none", TYPE: String

-of OUTPUT_FILE, --output_file OUTPUT_FILE
Provide a path and an output file, e.g. "/path/to/the/target_file".
Default Value: STDOUT, TYPE: String

--name NAME
Defines a name which is used in the sequence output for each entity
Default Value: antaRNA_, TYPE: String

-ov, --output_verbose
Displayes intermediate output on the STDOUT.

-v, --verbose
Prints additional features and stats to the headers of the produced sequences. Also adds the structure of the sequence. When using this flag, the fast format of the output is not provided anymore.

ACO Machanistic Variables

-a ALPHA, --alpha ALPHA
Sets alpha, probability weight for terrain pheromone influence during the calculation of the edge probabilities. Must be in the interval of [0,1]
Default Value: 1.0, TYPE: Float

-b BETA, --beta BETA
Sets beta, probability weight for terrain path influence during the calculation of the edge probability. Must be in the interval of [0,1].
Default Value: 1.0, TYPE: Float

-er ER, --ER ER
Pheromone evaporation rate.
Determines the rate on how much pheromone information evaporates in each round.
Default Value: 0.2, TYPE: Float

Structure constraint quality weighting factor withint the score calculation.
Default Value: 0.5, Range: [0,1], TYPE: Float

GC content constraint quality weighting factor. [0,1]
Default Value: 5.0, Range: [0,1],TYPE: Float

Sequence constraint quality weighting factor. [0,1]
Default Value: 1.0, Range: [0,1],TYPE: Float

Select the improving method. h=hierarchical, s=score_based.
Default Value: s, TYPE: String

-r RESETS, --Resets RESETS
Amount of maximal terrain resets, until the best solution is returned as solution.
Default Value: 5, TYPE: Integer

Delimits the convergence count criterion for a reset. If the threshold for this counter is exceeded, the terrain will be rest to its inital state.
Default Value: 130, TYPE: Integer

Ant threshold for termination. If x subsequent solutions do not improve the result anymore, this threshjold will termiate the program.
Default Value: 50, TYPE: Integer

Robert Kleinkauf 05/2015