I have a hundred insect genomes and I'm looking for repeated regions along these assemblies.

First of all, I thought of using RepeatModeler, only the most familiar among you know that it is not at all optimized software that requires a lot of resources and calculation time, which is therefore not feasible in my case.

One possible solution Repbase is not free.

I thought for example to use a blastn approach by using in query the assemblages and in database of nucleotide databases containing ETs, which would be an approach maybe less sensitive but much faster! Only I can't find a database in ET representative of eukaryotes

I have two questions:

  • Is there an alternative algorithm that is fast enough to process a large number of insect genomes?
  • Is there a database of representative ETs to enable a blastn style solution?

Thanks a lot.

  • $\begingroup$ when you say "ET" do you mean "TE" ("transposable element")? If not, what does that abbreviation stand for? $\endgroup$ – Maximilian Press Dec 15 '20 at 18:06
  • $\begingroup$ Yes Transposable element sorry $\endgroup$ – Grendel Dec 16 '20 at 8:34

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