Question: Bacterial genome annotation
1
gravatar for bird77
23 months ago by
bird7730
bird7730 wrote:

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.

genome • 865 views
ADD COMMENTlink modified 23 months ago by christopher medway440 • written 23 months ago by bird7730

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

ADD REPLYlink written 23 months ago by Asaf6.1k

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?

ADD REPLYlink written 23 months ago by bird7730

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.

ADD REPLYlink written 23 months ago by Joe14k
0
gravatar for Juke-34
23 months ago by
Juke-342.6k
Sweden
Juke-342.6k wrote:

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

ADD COMMENTlink written 23 months ago by Juke-342.6k
0
gravatar for christopher medway
23 months ago by
Cardiff, UK
christopher medway440 wrote:

RAST

ADD COMMENTlink written 23 months ago by christopher medway440
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