Bacterial genome annotation

Question

[bird77]

What tools can I use for the annotation for bacterial genomes (complete and/or draft genomes)?

I liked prokka very much but I have the feeling that the annotation is unreliable. I cross-checked a few entries via blast and it was not very accurate for the genes I looked for.

Any advice? Thank you.

[Asaf]

Are you sure you used prokka properly? You can specify a blast database to make predictions more accurate. I would have suggested prodigal for gene annotation but it's included in prokka

[bird77]

Thank you for the hint. How do I find the specific database for an organism and how can I integrate it in the prokka call?

[Joe]

What organism is it? Prokka is only as good as the databases it uses, so if it’s an unknown organism, you might get dodgy results.

Answer 1

[Juke34]

You can use genemark.hmm prokaryotes for the structural part. Then you may add the functions using interpro.

Answer 2

[christopher medway]

RAST