Transposon Scan?

Question

[Cacau]

Is there any software that can help to filter transposon-like sequences? I think there might be two cases. One is that it can tell TE given protein sequences. The other is that it works when DNA sequences are given since it can tell insertion motifs.

Answer 1

[cts]

I think that repeatmasker is what you want

Answer 2

[gammyknee]

Censor is another

Answer 3

[wadunn83]

If you are working in insects than you might want to take a look at TEfam. The focus is on mosquitoes but with blast you should be able to use it in most of the Dipetra.