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Best tool to annotate open reading frames (ORFs) in virus metagenomics?

Hi all! In your opinion, which is the best tool to anotate ORFs in viral metagenomics? I have some tick samples I want to do the viral characterization of, however I was told to annotate the ORFs with Geneious Prime, but I can´t afford it so, which is the next best option?

dna virus metagenomics
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updated by Ram Ram • written by maria.seg • maria.seg

1 answer

I have never worked with Geneious Prime so what I am about to say might be my bias talking rather than an informed opinion. Commercial programs of that type are rarely best tools for anything other than being most convenient for the users who want to use a point-and-click interface. So count yourself lucky that you can't afford it.

There are many databases of virus-specific hidden Markov models (HMMs) that can annotate most viral ORFs. In order to use them you will need to download HMM files from the links below, and use HMMer for annotation.

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written by Mensur Dlakic Mensur Dlakic

Thank you so much! I will try using HMMer

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written by maria.seg • maria.seg

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