Question: Bacterial Ontology or Annotation
gravatar for bkellman
3.5 years ago by
bkellman10 wrote:

I am interested in adding some functional analysis to my metagenomic study. Coming from a human gene expression background, I am wondering if there is a species or genus level ontology or annotation of bacteria I could use to gather and organize this functional information.

Thanks, Ben

ADD COMMENTlink modified 3.5 years ago by bongok40 • written 3.5 years ago by bkellman10
gravatar for natasha.sernova
3.5 years ago by
natasha.sernova3.7k wrote:

Concering bacterial annotation see this post, it has many useful links:

A Quick Way To Annotate Entire Bacterial Genomes To Go?

See also these three papers about bacterial ontology and metagenomivs:

Methodology and Ontology in Microbiome Research, 2014

Applying the Gene Ontology in microbial annotation

Metagenomics and biological ontology

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by natasha.sernova3.7k
gravatar for bongok
3.5 years ago by
bongok40 wrote:

There are many tools out there for annotating bacterial/archaeal genomes. My suggestion is to try multiple tools and do a comparison, especially if your analysis is hypothesis-driven.

For quick annotation (in the matter of minutes) - my suggestion would be prokka

For fairly quick and ease in visualization in terms of metabolic pathways (in the matter of hours) - I feel like blastkoala is pretty good.

For detailed annotation but may not be as rigorous - RAST is quite neat.

For rigorous and publication quality - IMG/ER would be my recommendation but the caveat is the time. IMG/ER only does one annotation a month and if you missed the queue, you may have to wait up to a month.

ADD COMMENTlink written 3.5 years ago by bongok40
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