Question: Bacterial genome annotation
1
gravatar for bird77
3.4 years ago by
bird7770
bird7770 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 • 1.2k views
ADD COMMENTlink modified 3.4 years ago by christopher medway450 • written 3.4 years ago by bird7770

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 3.4 years ago by Asaf8.5k

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 3.4 years ago by bird7770

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 3.4 years ago by Joe19k
0
gravatar for Juke34
3.4 years ago by
Juke345.2k
Sweden
Juke345.2k wrote:

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

ADD COMMENTlink written 3.4 years ago by Juke345.2k
0
gravatar for christopher medway
3.4 years ago by
Cardiff, UK
christopher medway450 wrote:

RAST

ADD COMMENTlink written 3.4 years ago by christopher medway450
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