Hi all,

We are looking for active infection of RNA viruses in metatranscriptomes of complex environmental communities.

What sequences would you use to find active retroviral infections?

When apply BLASTp vs the nr protein database on our viral RdRP candidate protein sequences, we find a lot of cellular matches. This fact makes us think that there could be some endogenous retroviruses that are annotated as "cellular" in nr.

Thoughts?

Thank you,

Guillermo