antaRNA (version 1.1)

Structure constraint using RNA dotbracket notation with fuzzy block constraint. (-Cstr):

Objective target GC content in [0,1]. (-tGC):

Number of sequences which shall be produced. (-n):

Allowing GU base pairs. (-GU):

Provides a seed value for the used pseudo random number generator. (-s):

Select the improving method. h=hierarchical, s=score_based. (-ip):

Amount of maximal terrain resets, until the best solution is retuned as solution. (-r):

Delimits the convergence count criterion for a reset. (-CC):

Delimits the amount of internal ants for termination convergence criterion for a reset. (-aTC):

Switch to pseudoknot based prediction using pKiss. Check the pseudoknot parameter usage!!! (-p):

Enable optimized parameters for the usage of pseudo knots (Further parameter input ignored). (-pkPar):

Defining the pKiss folding strategy. (--strategy):

Provides a maximum tGC value [0,1] for the case of uniform distribution sampling. The regular tGC value serves as minimum value. (-tGCmax):

Provides a tGC variance (sigma square) for the case of normal distribution sampling. The regular tGC value serves as expectation value (mu). (-tGCvar):

Provides a temperature for the folding algorithms. (-t):

Changes the energy parameterfile of RNAfold. If using this explicitly, please provide a suitable energy file delivered by RNAfold. (-P):

Provide a path and an output file, e.g. "/path/to/the/target_file". (-of):

Sequence constraint using RNA nucleotide alphabet {A,C,G,U} and wild-card "N". (-Cseq):

Sets the level of allowed influence of sequence constraint on the structure constraint [0:no influence; 3:extensive influence]. (-l):

Defines a name which is used in the sequence output. (--name):

Sets alpha, probability weight for terrain path influence. [0,1] (-a):

Sets beta, probability weight for terrain pheromone influence. [0,1] (-b):

Pheromone evaporation rate. (-er):

Structure constraint quality weighting factor. [0,1] (-Cstrw):

GC content constraint quality weighting factor. [0,1] (-Cgcw):

Sequence constraint quality weighting factor. [0,1] (-Cseqw):

Displayes intermediate output. (-v):

Prints additional output to the headers of the produced sequences. (-ov):

antaRNA - ant assembled RNA

antaRNA uses the VIENNNA RNA Package
- specifically it uses RNAfold and RNAdistance to calculate energies of and distances between secondary structures (version 2.1.x)
- for the parametrization of antaRNA the version 2.1.3 of the ViennaRNA package was used
For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/

Example parameters:

--Cstr "...(((...)))..." --tGC 0.5 -n 2
--Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov
--Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10