Description of feature
Dear DRAM-v developers,
Thank you so much for developing and maintaining this powerful tool for viral genome annotation and AMG prediction.
I recently read the paper A call for caution in the biological interpretation of viral auxiliary metabolic genes (https://doi.org/10.1038/s41564-025-02095-4), which advocates expanding our view of virus-encoded auxiliary genes beyond metabolic functions. The authors propose the broader concept of auxiliary viral genes (AVGs), under which AMGs are only one subclass involved in metabolism. Other categories include auxiliary physiology genes (APGs) and auxiliary regulatory genes (AReGs), which also play important roles in host physiology, regulation, and viral–host interactions.
In my current analysis, I noticed that many interested KOs are not present in amg_database.tsv, likely because they lack direct metabolic potential. Under this expanded AVG framework, I am interested in identifying these non-metabolic auxiliary viral genes using DRAM-v.
I would greatly appreciate your advice on whether it is reasonable to:
Retain genes with auxiliary scores 1–3 (high-confidence viral genes), and
Relax the strict filtering flags originally designed for AMGs
to systematically detect potential AVGs from existing DRAM-v annotation outputs?
Thank you very much for your time and insights.
Best regards.
Description of feature
Dear DRAM-v developers,
Thank you so much for developing and maintaining this powerful tool for viral genome annotation and AMG prediction.
I recently read the paper A call for caution in the biological interpretation of viral auxiliary metabolic genes (https://doi.org/10.1038/s41564-025-02095-4), which advocates expanding our view of virus-encoded auxiliary genes beyond metabolic functions. The authors propose the broader concept of auxiliary viral genes (AVGs), under which AMGs are only one subclass involved in metabolism. Other categories include auxiliary physiology genes (APGs) and auxiliary regulatory genes (AReGs), which also play important roles in host physiology, regulation, and viral–host interactions.
In my current analysis, I noticed that many interested KOs are not present in amg_database.tsv, likely because they lack direct metabolic potential. Under this expanded AVG framework, I am interested in identifying these non-metabolic auxiliary viral genes using DRAM-v.
I would greatly appreciate your advice on whether it is reasonable to:
Retain genes with auxiliary scores 1–3 (high-confidence viral genes), and
Relax the strict filtering flags originally designed for AMGs
to systematically detect potential AVGs from existing DRAM-v annotation outputs?
Thank you very much for your time and insights.
Best regards.