Use when searching protein sequences against conserved domain databases like CDD using reverse position-specific BLAST
rpsblast -query <input> -db <rpsdb> -out <output> -outfmt 6/home/vimalinx/miniforge3/envs/bio/bin/rpsblastreferences/help.mdrpsblast when the target is a reverse-position-specific domain database, not a general protein sequence database.deltablast when you want domains to seed a PSSM and then search a protein database.# 1) Standard conserved-domain annotation run
rpsblast \
-query proteins.fa \
-db cdd_db \
-outfmt "6 qaccver saccver evalue bitscore qstart qend sstart send qcovhsp" \
-evalue 1e-3 \
-max_target_seqs 20 \
-num_threads 8
# 2) Keep BLAST comments in the output for easier manual review
rpsblast \
-query proteins.fa \
-db cdd_db \
-outfmt 7
hmmscan or deltablast when the database or sensitivity assumptions differ.-db must point to an RPS/PSSM domain database rather than a standard BLAST protein DB.-help rather than --help; --version also errors in this BLAST+ build.-remote is incompatible with local threading.-outfmt, -evalue, and -max_target_seqs explicitly for reproducible annotation pipelines.