(Queery) Posible effectiveness at identifying autonomos class II TE?

INTABiotechMJ / MITE-Tracker

MITE Tracker: An accurate approach to identify miniature inverted-repeat transposable elements in large genomes

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(Queery) Posible effectiveness at identifying autonomos class II TE? #9

Open HSSTOM001 opened 3 years ago

HSSTOM001 commented 3 years ago

This looks like a great resource! I'm looking at prokaryotic transposons and I'm interested to know if MITE-Tracker has ever been tried on larger, autonomous, class II TEs? And specifically whether specifying a large maximum length (>10kb) would have any obvious issues? Thanks!

jacopoM28 commented 2 years ago

Hi,

since I am doing the same thing (even if preceded by a transposase tblastn to isolate possible autonomous insertions) I was wondering if you finally succeeded. I believe I have obtained good first results, but in the GFF file the elements are fewer than expected (maybe because of the filtering step of the software?), while in the candidates more. I was therefore a bit doubtful about which of the two outputs to use.

Cheers,

Jacopo

juancresc commented 1 year ago

I think that for a different kind of TEs you'd need to consider different things. First what type of TE is it? Are these TEs identificable only by their structure? is the structure of the element the same as a MITE? What else do we need to filter or stop filtering?