Transposable Element Annotation in fungi

[kajsa]

Hi there,

is there anyone of you who has experience of annotating transposable elements in fungi? I was thinking of using the REPET package (Flutre et al. 2011). Anyone having any experience of this package? Are there any other good alternatives?

Thank you in advance!
Kajsa

[colindaven]

I have tried Tedna which is simple to run and delivers results in a convenient format, fasta I think. I am not sure how complete the results are on a large plant genome though since I have not tested others yet.

I haven't tried REPET yet.

[kajsa]

Tedna, didn't hear about that before. Thanks!

[kajsa]

Do you know if the best method to find TEs is directly from unassembled reads or from an already assembled genome?

Thank you in advance!