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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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Question on output inlA genes #470

Open scotan opened 4 years ago

scotan commented 4 years ago

Hi,

I have a question about the output genes. I used Prokka to predict listeria genes and I have many inlA genes predicted (inlA-1, inlA-2, inlA-3 ...). I am getting confused on how to interpret this information. Where can I find information about this inlA subtypes? And is it possible to get all these inlA genes in a single genome? I am trying to match this information with the virulent inlA that is predicted by VirulenceFinder but I am not sure which inlA is the one corresponding to the virulent inlA.

Thank you very much, Anna

tseemann commented 4 years ago

I am not able to advise on matters of genetics or pathogenicity.

That said, to help I would need the full prokka.log file, and possbily the contigs.fa themselves.

The inlA gene only occurs once in the database. The inlA_1 (not inlA-1) would appear in Prokka if there were lots of broken pieces of it, or gene duplications.