Viral genome annotation · Biostar

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Viral genome annotation

Hi all,

I have got some viral genomes (using MARVEL) isolated from metagenomics data. I am wondering what programs I can use for functional annotation and taxonomic classifcation for the viral genomes?

I have used PROKKA (specified --kingdom viruses) and eggnogmapper for annotation but I am sure there are programs out there that specifically works on viruses.

Cheers and many thanks

Alan

viral genome annotaiton virus genome metagenomics

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updated 6.8 years ago by Joseph Hughes

• written 6.8 years ago by h.l.wong

There are few tools for virus annotation in that list https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/annotation_tools_genome.md

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written 6.8 years ago by Juke34

Thank you for your suggestion!

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written 6.7 years ago by h.l.wong

1 answer

Viruses are super diverse and range hugely in size and the number of genes. Tools that I have found useful for annotation of viruses are RATT, VaPiD and VGas. Each has pros and cons. I would maybe suggest starting with VAPiD but then I am not too sure what your data is like, specifically how novel your virus is.

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written 6.8 years ago by Joseph Hughes

Thanks! I don't know if the viruses are novel cause I have no idea what programs to classify them. I will try the programs you suggest.

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written 6.7 years ago by h.l.wong

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