1 .TH "Kinfold" "1" "1.1" "Christoph Flamm, Ivo Hofacker" "RNA"
4 Kinfold \- Simulate kinetic folding of RNA secondary structures
7 Kinfold [\fIOPTIONS\fP] < \fIinput\fP
11 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.
13 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.
15 Output consists of trajecotires (written to stdout) as well as a log file containing summary information for each trajectory.
20 \fBMove set options\fR
26 forbid structures containing isolated base-pairs
28 \fBSimulation options\fR
31 Number of trajectories to compute (default=1).
33 \fB\-\-time\fR<\fItmax\fP>
34 Set maximum length of folding trajectory. The default (500) is very short and meant for testing purposes only.
36 \fB\-\-grow\fR <\fIrate\fP>
37 Simulate folding during transcription with a chain growth event taking place every \fIrate\fP timesteps.
39 \fB\-\-glen\fR <\fIlen\fP>
40 Start a folding during transcription simulation with an inital chain length of \fIlen\fP.
43 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.
46 Read a start conformation from stdin, otherwise the open chain is used as start structures.
49 Read one or more stop structures from stdin, otherwise the MFE structure is used.
52 Use the Metropolis rule for rate between two neighboring conformations, i.e. k=min{1,exp(\-dE/RT)}. By default Kinfold uses the symmetric Kawasaki rule k=exp(\-dE/2RT).
54 \fB\-\-seed\fR<\fIstring\fP>
55 Specify the random number seed for the simulation. The seed \fIstring\fP 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.
59 \fB\-v\fR or \fB\-\-verbose\fR
60 Print more information to stdout.
62 \fB\-q\fR or \fB\-\-silent\fR
63 Do not write trajectories to stdout.
66 Don't print complete trajectory, but only local minimas encountered.
68 \fB\-\-cut\fR<\fIenergy\fP>
69 Print only those parts of the trajectory that stays below \fIenergy\fR.
71 \fB\-\-log\fR<\fIfile\fP>
72 Set the log file to \fIfile.log\fR. Default "kinout".
74 \fBEnergy model\fR see e.g. the Vienna RNA documentation for details
76 \fB\-\-dangles\fR<\fIint\fP>
77 Select dangling end model. Possible values "0" (none), "1" (normal), "2" (simplified)
79 \fB\-\-T, \-\-Temp\fR<\fItemp\fP>
80 Set simulation temperature to \fItemp\fP degrees centigrade.
82 \fB\-P, \-\-Par\fR <\fIfilename\fP>
83 read energy\-parameters from \fIfilename\fP.
86 use logarithmic multiloop energies instead of linear. Default is on, i.e. using \-\-logML switches log energies off.
91 Output help information and exit.
94 Output version information and exit.
99 Start structure is open chain, stop structure is MFE structure.
100 The example output below is a possible trajectory for the sequence ACUGAUCGUAGUCAC.
103 Kinfold \-\-time 100000 < seq.in
104 ............... 0.00 2.660
105 ....(......)... 4.80 2.664
106 ...((......)).. 0.70 2.760
107 ..(((......))). 0.20 3.407
108 ..((((....)))). \-0.60 3.579 X1
111 The trajectory lists stucture, energy, and time for each simulation step. The X1 signifies that the trajectory terminated in the first stop structure.
112 In addition the logfile kinout.log would contain information needed to reproduce the simulation results such as options and random seeds used.
114 #Date: Tue Oct 7 10:24:27 2008
115 #EnergyModel: dangle=2 Temp=37.0 logML=logarithmic Par=(null)
116 #MoveSet: noShift=off noLP=off
117 #Simulation: num=2 time=500.00 seed=clock fpt=on mc=Kawasaki
118 #Simulation: phi=1 pbounds=0.1 0.1 2
119 #Output: log=kinout silent=off lmin=off cut=20.00
121 #............... ( 0.00)
122 #..((((....)))). ( \-0.60) X01
123 (20773 2191 29311) X01 3.579
126 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.
128 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
130 Kinfold \-\-grow 100000 \-\-glen 10 < seq.in
134 Christoph Flamm <xtof@tbi.univie.ac.at>
136 Ivo Hofacker <ivo@tbi.univie.ac.at>
139 The Vienna RNA package http://www.tbi.univie.ac.at/~ivo/RNA