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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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