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RNAXPLORER(1) User Commands RNAXPLORER(1) NAME RNAxplorer - manual page for RNAxplorer 0.9.0 SYNOPSIS RNAxplorer [OPTION]... DESCRIPTION RNAxplorer 0.9.0 The RNAxplorer is a multitool, that offers different sampling and clus- tering methods to explore RNA energy landscapes. The RNAxplorer is a multitool, that offers different methods to explore RNA energy landscapes. In default mode (or with -M RSH option) it takes an RNA sequence as input (either stdin or --sequence parameter) and outputs sampled secondary RNA structures. The repellant sampling heuristic iteratively penalizes base pairs of local minima of struc- tures that have been seen too often. This results in a diverse sample set with the most important low free energy structures. Another important sampling method (-M RS option) is based on reference structures (--struc1 and --struc2). This method produces structures in the vicinity of these two reference structures. Arbitrary many refer- ences can be added if a fasta file is used as input (via stdin). Often the output of sampling methods has to be coarse grained by local minima that are defined by a gradient walk. A parallelized gradient descent procedure can be used to retrieve local minima (-M RL option) of sam- pled structures (input via stdin). -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 General Options: Below are command line options which alter the general behavior of this program -v, --verbose Be verbose (default=off) Repulsive Sampling Options: --sequence=STRING Input sequence (default=`') --penalize-structures Penalize structures instead of base pairs of local minima, that occure too often. (default=off) --struc1=STRING Input structure 1 (default=`') --struc2=STRING Input structure 2 (default=`') --granularity=INT Granularity, i.e. number of samples after which distortion checks are performed (default=`100') -n, --num-samples=INT Number of samples in total. The number of samples per iteration is n/g. (default=`100000') -f, --exploration-factor=FLOAT Exploration factor (default=`1') --min-exploration-percent=FLOAT Minimum exploration percentage before adding new repelled structures (default=`1') --cluster Cluster resulting local minima to reduce effective size (de- fault=off) --lmin-file=STRING Output filename for local minima (default=`') --TwoD-file=STRING Output filename for pseudo-2D file (default=`') --nonred Do sampling with non-redundant pbacktrack (default=off) --nonred-file=STRING Input filename for nonredundant samples (default=`') -2, --explore-two-neighborhood Explore 2-Neighborhood of local minima, i.e. eliminate shallow minima (default=off) --post-filter-two Post processing Filter local minima according to 2-Neighborhood, i.e. eliminate shallow minima (default=off) --ediff-penalty Use energy difference instead of kT for penalty (default=off) --mu=FLOAT proportion factor used to decide whether sampling round was suf- ficient (default=`0.1') Algorithms: Select additional algorithms which should be included in the calculations. Default is the repellant sampling heuristic. Dis- play more options with --detailed-help. -M, --method=<method> Set the method used to obtain meshpoint structures for the bi- section algorithm (default=`RSH') Available options are: GW Gradient Walk (default) MC Monte Carlo walk MC-SA Monte Carlo Walk with simulated Annealing DB-MFE Distance based MFE structure meshpoints TRATES Transition rate computation SM Stochastic sampling method with 2D mapping (activate distortion with -e"N"). RS Repellant or Attraction sampling RSH Repellant sampling heuristic RL Retrieve local minima. Standard input should be a sequence and a set of secondary structures (one per line). \ --betaScale=DOUBLE Set the scaling of the Boltzmann factors (default=`1.') The argument provided with this option enables to scale the thermodynamic temperature used in the Boltzmann factors indepen- dently from the temperature used to scale the individual energy contributions of the loop types. The Boltzmann factors then be- come exp(-dG/(kT*betaScale)) where k is the Boltzmann constant, dG the free energy contribution of the state and T the absolute temperature. -e, --extended_opt=STRING Some extended options: N normal distortion (no shift) B alter both potentials at once R relax potential instead of increasing it S shift potential to other structure F shift to first structure V verbose (default=`') -i, --iterations=INT Set the number of iterations/simulations (default=`1') -m, --maxKeep=INT maxKeep for direct path search (default=`10') -s, --maxStore=INT amount of best solutions to hold per iteration (default=`10') -r, --remember=INT Set the number of structure states to remember in a TABU list (default=`10') -c, --circ Assume a circular (instead of linear) RNA molecule. (default=off) --cooling-rate=FLOAT Cooling factor used for simulated annealing (default=`0.9998') --tstart=FLOAT start temperature in deg. Celcius (default=`37.0') --tstop=FLOAT stop temperature in deg. Celcius (default=`0.0') --penalizeBackWalks Add a penalty for backward moves, i.e. moves along states al- ready visited (default=off) --basinStructure just perform a gradient walk starting from a given structure (default=off) -D, --maxD=INT Maximum base pair distance between meshpoints and references (default=`5') --maxD1=INT Maximum base pair distance between meshpoints and reference structure 1 (default=`5') --maxD2=INT Maximum base pair distance between meshpoints and reference structure 2 (default=`5') Model Details`: -T, --temp=DOUBLE Rescale energy parameters to a temperature of temp C. Default is 37C. --p0=STRING Set the percentage of the references distortion value <int> to <double> Can be given for all reference indices (NOTE: the value <double> should be between 0 and 1) (example: "--p0 2=0.5" - distortion value of sequence 2 will be multiplied with 0.5 be- fore sampling.) Gradient walker options`: --shift_moves Use shift moves for gradient walks. (default=off) -P, --parameter_file=STRING Use the given parameter file for gradient walks. RNAxplorer 0.9.0 October 2024 RNAXPLORER(1)
NAME | SYNOPSIS | DESCRIPTION
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