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tseemann / barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor
GNU General Public License v3.0
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Barrnap 0.8 issues with 18S sequences #20

Closed tseemann closed 6 years ago

tseemann commented 7 years ago

Hi Torsten,

I recently installed the latest version of Barrnap (0.8) and tested it by running it on a fasta file containing 18S sequences that I downloaded from SILVA. It detected partial 16S sequences when —kingdom was set to bac or arc, but detected zero ribosomal RNA features when —kingdom was set to euk.

However, Barrnap 0.7 was able to detect the 18S sequences in my fasta file (with an e-vaue of 0, as was expected). I didn’t investigate the matter further (I’m mainly a wet lab biologist with some bioinformatics skills) - but I wanted to bring the matter to your attention.

Best Regards, Mahwash Jamy (Institute of Organismal Biology Uppsala University Sweden)

tseemann commented 7 years ago

It seems the euk.hmm file does not contain an 18S model anymore - there was a bug in my build script. I am working on a fix.

tseemann commented 6 years ago

I seem to have fixed this.