Question: Prokka Annotation for Bacterial Transcriptomes
gravatar for gabriel.jabud
10 months ago by
United States
gabriel.jabud30 wrote:

Can Prokka be used to annotate bacterial transcriptomes? Say I have a fasta file generated from a de novo assembly (Trinity). Will using Prokka the same way you annotate genomes work correctly? I don't see any mention of transcriptomes in the Prokka documentation, but it seems like it should work the same.

If not, what tool does everyone use to annotate bacterial transcriptomes?

ADD COMMENTlink modified 10 months ago by natasha.sernova3.7k • written 10 months ago by gabriel.jabud30

See this post below but it doesn't give a final solution to your question.

It shows a direction to continue your project.

Prokka bacteria genome annotation

This second post shows, that people do use Prokka, but they have some doubts about.

Bacterial genome annotation

And the post suggests some alternative.

The third post provides another way.

Is there a way to run RAST annotation locally?

You have to choose.

ADD REPLYlink modified 10 months ago • written 10 months ago by natasha.sernova3.7k

Find the ORFs in your transcripts (e.g. with transdecoder) and then blastx (or translate and blastp) against a bacterial protein database. Transcripts without ORFs and those without hits you could process with RNA finding tools (tRNAscan, Infernal, SortmeRNA etc.) and blastn against ncRNA databases. No need to do gene finding.

ADD REPLYlink written 10 months ago by cschu1812.0k

In theory, I can’t see any reason this wouldn’t work. The annotations may not be fantastic however if it’s quite a broken up set of sequences etc.

ADD REPLYlink written 10 months ago by Joe16k
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