How are transposable elements determined?

bobeobibo / phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

MIT License

46 stars 15 forks source link

How are transposable elements determined? #18

Closed snayfach closed 4 years ago

snayfach commented 4 years ago

I couldn't find this information in the publication.

Thanks, Stephen

bobeobibo commented 4 years ago

We mark possible transposable element insertions if we detect more than two consecutive transposases or integrases inside the prophage. Integrases and transposases are determined according to custom pVOG HMM lists.

We added this feature because TE can massively integrate into prophages (or anywhere, actually...) and possibly interrupt their genomic structure. We think this is what the microbiologists should be aware of when exploring prophages.