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Kinfold(1) RNA Kinfold(1) NAME Kinfold - Simulate kinetic folding of RNA secondary structures SYNTAX Kinfold [OPTIONS] < input DESCRIPTION The program Kinfold simulates the stochastic folding kinetics of RNA sequences into secondary structures. Folding trajectories are simulated using a Monte Carlo procedure using the formation, and dissociation of individual base pairs, and (optionally) the shifting of individual base pairs. For the energy evaluation of RNA secondary structures Kinfold uses routines from the Vienna RNA Package. Input is read from stdin and consists of an RNA sequence, optionally followed by the initial structure and one or more stop structures in dot-bracket notation. Output consists of trajecotires (written to stdout) as well as a log file containing summary information for each trajectory. OPTIONS Move set options --noShift turn of shift moves. --noLP forbid structures containing isolated base-pairs Simulation options --num Number of trajectories to compute (default=1). --time<tmax> Set maximum length of folding trajectory. The default (500) is very short and meant for testing purposes only. --grow <rate> Simulate folding during transcription with a chain growth event taking place every rate timesteps. --glen <len> Start a folding during transcription simulation with an inital chain length of len. --fpt Toggles between first passage time calculations that end as soon a stop struicture is reached and open-ended simulations. Since the default is "first passage time", i.e. using the --fpt switches to open ended simulation. --start Read a start conformation from stdin, otherwise the open chain is used as start structures. --stop Read one or more stop structures from stdin, otherwise the MFE structure is used. --met Use the Metropolis rule for rate between two neighboring confor- mations, i.e. k=min{1,exp(-dE/RT)}. By default Kinfold uses the symmetric Kawasaki rule k=exp(-dE/2RT). --seed<string> Specify the random number seed for the simulation. The seed string consists of three numbers separated by an equal sign, e.g. 123=456=789. If no seed is specified it is derived from the system clock at program start. Output options -v or --verbose Print more information to stdout. -q or --silent Do not write trajectories to stdout. --lmin Don't print complete trajectory, but only local minimas encoun- tered. --cut<energy> Print only those parts of the trajectory that stays below en- ergy. --log<file> Set the log file to file.log. Default "kinout". Energy model see e.g. the Vienna RNA documentation for details --dangles<int> Select dangling end model. Possible values "0" (none), "1" (nor- mal), "2" (simplified) --T, --Temp<temp> Set simulation temperature to temp degrees centigrade. -P, --Par <filename> read energy-parameters from filename. --logML use logarithmic multiloop energies instead of linear. Default is on, i.e. using --logML switches log energies off. Generic options --help Output help information and exit. --version Output version information and exit. EXAMPLES default mode: Start structure is open chain, stop structure is MFE structure. The example output below is a possible trajectory for the sequence ACUGAUCGUAGUCAC. Kinfold --time 100000 < seq.in ............... 0.00 2.660 ....(......)... 4.80 2.664 ...((......)).. 0.70 2.760 ..(((......))). 0.20 3.407 ..((((....)))). -0.60 3.579 X1 The trajectory lists stucture, energy, and time for each simulation step. The X1 signifies that the trajectory terminated in the first stop structure. In addition the logfile kinout.log would contain informa- tion needed to reproduce the simulation results such as options and random seeds used. #Date: Tue Oct 7 10:24:27 2008 #EnergyModel: dangle=2 Temp=37.0 logML=logarithmic Par=(null) #MoveSet: noShift=off noLP=off #Simulation: num=2 time=500.00 seed=clock fpt=on mc=Kawasaki #Simulation: phi=1 pbounds=0.1 0.1 2 #Output: log=kinout silent=off lmin=off cut=20.00 #ACUGAUCGUAGUCAC #............... ( 0.00) #..((((....)))). ( -0.60) X01 (20773 2191 29311) X01 3.579 ( 7439 25635 52414) Note that all times are given in internal units that can be translated into real time only by copmparison with experiment. Very roughly one time step corresponds to about 1e-7 seconds. To run a folding during transcription simulation use the --grow option. Assuming a transcription rate of 100 nt/sec and 1 sec about 1e7 time steps we could use Kinfold --grow 100000 --glen 10 < seq.in AUTHORS Christoph Flamm <xtof@tbi.univie.ac.at> Ivo Hofacker <ivo@tbi.univie.ac.at> SEE ALSO The Vienna RNA package http://www.tbi.univie.ac.at/~ivo/RNA Christoph Flamm, Ivo Hofacker 1.1 Kinfold(1)
NAME | SYNTAX | DESCRIPTION | OPTIONS | EXAMPLES | AUTHORS | SEE ALSO
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