Question: Bacterial genome annotation
1
gravatar for bird77
17 months ago by
bird7720
bird7720 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 • 709 views
ADD COMMENTlink modified 17 months ago by christopher medway420 • written 17 months ago by bird7720

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 17 months ago by Asaf5.3k

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 17 months ago by bird7720

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 17 months ago by jrj.healey11k
0
gravatar for Juke-34
17 months ago by
Juke-342.0k
Sweden
Juke-342.0k wrote:

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

ADD COMMENTlink written 17 months ago by Juke-342.0k
0
gravatar for christopher medway
17 months ago by
Cardiff, UK
christopher medway420 wrote:

RAST

ADD COMMENTlink written 17 months ago by christopher medway420
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