Use when searching nucleotide sequences against protein domain profile databases (PSSMs) to detect conserved domains via position-specific scoring.
rpstblastn -query <nucleotide.fasta> -db <pssm_db> -out <results.out>/home/vimalinx/miniforge3/envs/bio/bin/rpstblastnreferences/help.mdrpsblast if the query is already protein, and blastx if the target is a full protein sequence database rather than a domain database.# 1) Standard translated domain search against a PSSM database
rpstblastn \
-query contigs.fa \
-db cdd_db \
-query_gencode 11 \
-outfmt "6 qaccver saccver evalue bitscore qstart qend sstart send qcovhsp" \
-evalue 1e-3 \
-max_target_seqs 20 \
-num_threads 8
# 2) Restrict the search to one query strand
rpstblastn \
-query contigs.fa \
-db cdd_db \
-strand plus \
-outfmt 7
-db must be a PSSM/profile database, not a standard nucleotide or protein BLAST DB.-help rather than --help; --version errors in this BLAST+ build.-remote is incompatible with local threading.-query_gencode, -strand, -outfmt, and -evalue deliberately.