? program to simulate spread of transposon in a population?

bob deboy deboy at welchlink.welch.jhu.edu
Wed Dec 21 10:20:15 EST 1994


I am a graduate student studying a bacterial transposable element, Tn7.
This is how I score transposition of Tn7 from a plasmid to the chromosome:

1. Start with a single cell      (Tn7 in plasmid, not in chromosome)
2. Grow-out a clonal population  (Tn7 can transpose to chromosome at any time)
3. Score fraction of progeny with a Tn7 insertion in the chromosome

So I know the fraction of progeny that have inherited a chromosome with or
without a Tn7 insertion.
But I don't know when the transposition event(s) actually occurred during
the grow-out. That is, at what generation(s) did the transposition(s)
occur?



MY QUESTIONS:

Are there computer programs that can simulate my transposition experiment?
I would like to be able to choose the frequency of transposition per
generation and observe the outcome. Hopefully, I'll at least be able to
rule out some models and be able to say when transposition could not have
occurred.

Perhaps I can test more sophisticated models, too. I'd like to know the
outcome if we vary the frequency of transposition during the experiment.
For example, probability = 0.001 until generation 4, then 0.01 until
generation 8, then back to 0.001. Again, I want to be able to rule out
models that don't fit my observations.

I've heard of the "game of life" program; could it work? 

Finally, my expertise is molecular biology, not computer programming. So
I'm hoping for a user friendly program. And of course, cool graphics would
make my day in the lab.



THANKS FOR YOUR HELP!

Bob DeBoy

deboy at welchlink.welch.jhu.edu
410-955-2731




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