jiarong/VirSorter2

Database update

blaizereal opened this issue · 1 comments

blaizereal commented

Dear jiarong,

Will you be able to update the database with the latest PFAM/HMM files? If not, is there any way to do it in-house?

Thanks: blaize

jiarong commented

Hi blaize, I am planning to do an overall database update but quite overwhelmed with other things now, so likely in summer. If you want to update Pfam on your own, you just need to update the following files in db/hmm/pfam/:

Pfam-A-Archaea.hmm
Pfam-A-Bacteria.hmm
Pfam-A-Eukaryota.hmm
Pfam-A-Mixed.hmm
Pfam-A-Viruses.hmm

The rule to define host domain is if >=90% seqs in a Pfam then it is that domain specific. Otherwise, it's "Mixed". Pfam seqs are from UniProt and you can find their taxonomy there.

  • 👍1