I am now searching for the position of transposable elements (TE) in the assembled whole-genome contigs of persimmon fruit (Diospyros Kaki).
Since there is not a transposable element database of such a species so rare of research interest, I have to use TE database from other plants (e.g. MIPS PlantsDB).
Therefore, questions related to alignment came to my mind :
1) How conserved are the sequences of transposable elements within plants in general, so the comparison of the genome sequence of one plant with TE from other plants is a valid method?
2) If you have hands-on experience of blasting genome sequence with a TE database, what options did you set to get a relatively conservative result that covers most of the possible true hit?
Thank you very much.