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Published 20 hours ago • verified publisher icon tseemann

rRNA not well annotated with Barrnap

Open ireneortega opened this issue 4 years ago • 5 comments

Hi Torsten,

I noticed Barrnap doesn't annotate well rRNA. My genomes have an intergenic spacer region of 150 bp in 23S rRNA and PROKKA annotates different CDS in that region. For that reason, no 23S rRNA is annotated in the genome, which is not correct. Could you please solve that?

Thanks!

ireneortega avatar Apr 21 '20 10:04 ireneortega

I have noticed that this has happened also to me. I have some bacteria strains annotated with prokka version 1.14.6 that have no 23S gene but some others annotated with v1.12 were ok. Did something change between these versions? Please I have to upload the annotation files to public databases and this is urgent to solve. Thank you

LRT-14 avatar Oct 13 '21 12:10 LRT-14

I usually use RNAmmer instead of Barrnap. For a reference genome I tested, RNAmmer found the same number as are in the NCBI annotation for that genome.

ireneortega avatar Oct 13 '21 15:10 ireneortega

Do you mean that RNAmmer works ok, but Barrnap doesn't?

LRT-14 avatar Oct 14 '21 06:10 LRT-14

For me, RNAmmer solved my issue. I'm not trying to verify tools. Try to execute both and analyse the results.

ireneortega avatar Oct 14 '21 18:10 ireneortega

Is RNAmmer still available outside of prokka?

jacquefm avatar Jul 03 '23 21:07 jacquefm