Transposable Elements Simulation

[Manuel Hoyos]

Hello everyone. Before asking my question, let me thank the group of developers for producing SLiM. It is a formidable work tool.

Now my question. 

Could you please indicate how to simulate an RNA transposon vs a DNA transposon in the same subpopulation? For me, the differentiation of these two classes in my simulation is of crucial relevance. Thank you very much and kind regards.

P.S: Please hold a SLiM workshop in Texas!

[Ben Haller]

Hi Manuel,

I'm afraid I don't know enough about transposons to be able to speak to this.  But speaking generally, modeling transposons in SLiM involves scripting (as in the recipe in section 14.12 of the SLiM manual).  So you'd just need to think about how you want your model to treat RNA vs. DNA transposons differently, and implement that in your script.  It is really up to you, as the writer of the script.  Starting with a design spec that you're written on paper, before you start scripting, can be helpful for clarifying what you want your script to do.  If you have a more specific question once you dig into the problem more, of course feel free to post another question here.  If you're not familiar with SLiM and Eidos scripting yet, starting with the SLiM Workshop (available for free online) is recommended.  In the meantime, perhaps you'll get a reply here from somebody who knows more about transposons than I do.  Happy modeling!

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University


Manuel Hoyos wrote on 10/20/24 1:02 AM:

--
SLiM forward genetic simulation: http://messerlab.org/slim/
---
You received this message because you are subscribed to the Google Groups "slim-discuss" group.
To unsubscribe from this group and stop receiving emails from it, send an email to slim-discuss...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/slim-discuss/fd140112-fbbe-499e-b608-fe4ebeef433bn%40googlegroups.com.

[annamaria....@gmail.com]

Hi Manuel, 

if your focus is on the different propagation mechanisms of DNA vs. RNA transposons (cut & paste vs. copy & paste), this is definitely doable thanks to the scriptability of SLiM. For example, you could define DNA and RNA transposons as different mutation types and then implement different "transposition rules" for these two types (i.e., remove the original TE if a transposition event has happened). I use SLiM to track transposon invasions in experimental fly populations: it is a rather simple model (only one TE type), but it works great :) As Ben pointed out, the SLiM online workshop and recipe 14.12 are a great way to get started! Good luck with your research! 

Best,

Anna 

[Manuel Hoyos]

Thank you, Dr. Haller. I will model as much as I can, and when I get stuck, I'll post again. Once again, thank you so much for designing this tool.