Use when searching protein sequences against profile hidden Markov models (HMMs) such as Pfam or other HMM databases.
hmmscan [-options] <hmmdb> <seqfile>/home/vimalinx/miniforge3/envs/bio/bin/hmmscanhmmscan when the query is sequence and the target is the HMM database.hmmpress for faster repeated scans.# 1) Scan proteins against a pressed HMM database
hmmscan \
--tblout hits.tbl \
--domtblout domains.tbl \
--cpu 8 \
Pfam-A.hmm \
proteins.fa
# 2) Use curated gathering thresholds from the database
hmmscan \
--cut_ga \
--domtblout domains.tbl \
Pfam-A.hmm \
proteins.fa
# 3) Produce smaller text output while keeping parseable tables
hmmscan \
--noali \
--tblout hits.tbl \
--domtblout domains.tbl \
Pfam-A.hmm \
proteins.fa
hmmpress if you will reuse it.-h for help; --help and --version are not valid here.--cut_ga, --cut_tc, and --cut_nc only make sense if the HMMs actually carry curated thresholds.--domtblout when domain boundaries matter; --tblout alone is not enough.