I'm using HMMER to find domains to a battery of viral contigs (in fasta file) against Pfam database. I'm not using MSAs because most of the contigs are not related so cannot be aligned. I used hmmscan first but the running speed is just too slow. I wanted to use hmmsearch but the query file needs to be in hmm profile format in order to fit in the hmmsearch program. If I were to use hmmbuild to convert this fasta file to hmm, it would require it to be MSA. So I'm kinda stuck in here.
So.. here's what it is : Is there anyway i can end up using hmmsearch instead of hmmscan for a non-MSA fasta file?