Tool for Phage/Virus gene prediction and annotation

Question

[DanielC]

Dear Friends,

Could you please suggest a promising tool for prokaryotic gene prediction and annotation? I have been using DNAMaster, but it comes with a GUI and not stable to work with. And, I am looking for a standalone method for prediction and annotation.

Thanks, DK

[natasha.sernova]

By the way, phages are viruses. They probably have different tools for gene prediction.

like this one A: What Are Some Good Interactive Circular Genome Browsers?

Answer 1

[lieven.sterck]

Prokka would be the first one that comes to mind and I guess most commonly used one as well

[lieven.sterck]

as pointed out by natasha.sernova , if the organism you are working on is a virus (phages) then prokka is likely not the most suitable tool

[Asaf]

In a lot of cases viral genes resemble host genes and a lot of bacterial genomes contain phages so prokka (prodigal actually) will find them. Other viruses' genes might not be detected by prokka

Answer 2

[Joe]

Try one of the following tools that Nick Waters benchmarked:

https://nickp60.github.io/weird_one_offs/testing_3_prophage_finders/

Phaster and ProphET are some of the more widely used. As with most predictors though, every tool gives you a different answer.

Take them with a grain of salt.

Answer 3

[Juke34]

A quick search on google talk about VAPiD or VIGOR.
Otherwise abinitio tools like GeneMark might do the job.