I would like to check transposable elements through a genome with a sliding window approach but I am not sure about which window and step size to use.

Is there a way to optimise the window size and step size when doing sliding window based operations? I mean how to choose which sizes to pick?


  • 1
    $\begingroup$ This question appears sparse on detail. What genome is this? What database of genomes? Traditionally a lot of work on transposable elements was performed on Drosophila. Also what is the algorithm for identifying transposons, e.g. via LTRs, blasting against a transposon database, or looking for the transposase protein or something else? $\endgroup$
    – M__
    Apr 20, 2022 at 0:25
  • $\begingroup$ This is rabbit genome (Orycun2.0). And basically I would like to check the correlation between transposable elements and nuclear insertions with mitochondrial origin (numts). In the corresponding literature there are informations about the window sizes used but not about the step sizes. $\endgroup$ Apr 20, 2022 at 5:53
  • 3
    $\begingroup$ I will reiterate @M__'s point: the sliding window technique refers not to a single algorithm but to a family of algorithms and procedures. It is very difficult for us to give you useful feedback if you don't provide more details on the tool(s) or approach(es) you are using. $\endgroup$ Apr 20, 2022 at 16:32
  • $\begingroup$ I just would like to repeat the same experiment as they did in this great article: mdpi.com/2075-4450/11/10/680/htm# in the 4th figure. Where the authors correlated the density distribution of numts and TEs. They provided the window size but not the step size. $\endgroup$ Apr 20, 2022 at 18:33


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