Identical results with --kingdom bac arc and euk

tseemann / barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor

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Identical results with --kingdom bac arc and euk #22

Closed snayfach closed 5 years ago

snayfach commented 6 years ago

Here are the commands I used:
barrnap $IN_PATH --threads 1 --kingdom euk barrnap $IN_PATH --threads 1 --kingdom bac barrnap $IN_PATH --threads 1 --kingdom arc

In all cases the following output is produced:

##gff-version 3
k85_159010  barrnap:0.8 rRNA    4717    4828    6.8e-10 -   .   Name=5S_rRNA;product=5S ribosomal RNA

It seems weird that the exact same evalue would be produced for searches against the 3 different hmm databases. How do I know which domain the 5S gene corresponds to?

tseemann commented 6 years ago

The 5S model is the same one in all those kingdoms. It's taken from Rfam and re-used. So identical results are expected.

Do you have reason to believe your species 5S rRNA is significantly different?