I've run both InterProScan and HMMER because im interested in pfam hits for a set of proteins. Interproscan was run like so:
./interproscan.sh -i my_prot.faa -f tsv
and then i filtered the results for pfam hits with E value < 0.001
HMMER was run like so:
hmmscan --tblout hmmer_result.txt -E 0.001 Pfam-A.hmm my_prot.faa
I compared the outputs and for some reason, InterProScan finds less proteins with pfam hits than HMMER (approximately 150 proteins less). I checked and they are both using the most recent pfam database (32.0) so I'm not sure why this could be happening. Any ideas ?