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tseemann / barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor
GNU General Public License v3.0
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Concatenating all .hmm for a "meta" search? #23

Closed bachev closed 6 years ago

bachev commented 6 years ago

Hi Torsten,

would it make sense to concatenate all db/*.hmm files to allow for a "meta" search?

Rationale: I have some eukaryotic RNASeq data and there one has rRNA from the cell as well as from the mitochondrion. And I would very much like not run barrnap twice (or more times for metagenomics) and then try to weed out by hand (i.e., by script) the most appropriate matches.

Best, B.

tseemann commented 6 years ago

@bachev that's a good question.

A simple concatenation will not work, as each kingdom shares some RNA subunits with others, but i've made kingdom-specific models for them. They have the same NAME in the .hmm files. So I would need to make kingdom part of the name to disambiguate them.

Secondly, I might have to be smarter how to select and filter competing matches.

I am looking into it.

tseemann commented 6 years ago

This is same as earlier #4 so I'll close this for now.