I was wondering if you can make a custom marker gene database as you can for genome database?
Related, I was curious as to why PVOG was not used as a database. I am not fluent on how each differs or if profiles from these other databases include PVOG?
I noticed that viral contigs I had assigned as phage by having at least 3 PVOG hits (evalue1e-5) did not have viral proteins predicted. Do you use a stricter criteria?
More curious than anything!
No it is not possible to create a custom HMM database at the moment. I didn’t use pVOG which is my experience is not as comprehensive as VOGDB and not up to date.
If you’d like more feedback, feel free to share more details on your phage in question, including the contig sequence, CheckV results, and pVOG results.