possible option for "prokaryotic" search (archaeal + procaryotic)?

[jvollme]

I was always wondering (also for rnammer and similar tools) why there always seems to be a strict rule to only search for archaeal OR bacterial rRNAs, but never for both at the same time?

I would guess that In most settings, whether it is to help identify an isolate, a SAG or a MAG, the actual use case for specifically only searching for bacterial OR archaeal rRNA sequences seems rather low. Especially since the hmm models of both kingdoms do seem to overlap quite a bit, and most people would align the obtained sequence to a reference database anyway, for an exact classification.

Wouldn't it perhaps be more practical to perform a combined search based on both bacterial AND archaeal models in one go, e.g. by simply concatenating the bacterial and archaeal models? Then each detected sequence could either just be assigned to the model (bacterial or archaeal) which yielded the highest score, or the exact classification could just be outright left to downstream BLAST analyses, which the user will most probably perform anyway.

Could this be relatively easy to implement (e.g. just combining the hmm-files for bacteria and archaea) or am i missing something fundamental here?