I have a metagenome assembly with ORFs predicted with prodigal and clustered with CD-HIT - resulting in a file with clusters of fasta headers and a normal unsorted fasta file.
I would like to search this against the pVOGs database (http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads.html). I've downloaded the pVOGS HMM profiles and tried to work out how to search against it but I can't make sense of the HMMER manual. I am doing this so I can filter out any contigs that doesn't have hits (or the hits are really sparse).
Thanks for helping in advance