rpstblastn

name	rpstblastn
description	Use when searching nucleotide sequences against protein domain profile databases (PSSMs) to detect conserved domains via position-specific scoring.
disable-model-invocation	true
user-invocable	true

rpstblastn

Quick Start

• Command: rpstblastn -query <nucleotide.fasta> -db <pssm_db> -out <results.out>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/rpstblastn
• Version: 2.17.0+
• Full reference: See references/help.md

When To Use This Tool

• Search nucleotide queries against conserved-domain PSSM databases without translating and extracting ORFs manually first.
• Detect protein-domain content in transcripts, contigs, or genomic intervals.
• Prefer rpsblast if the query is already protein, and blastx if the target is a full protein sequence database rather than a domain database.

Common Patterns

# 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

Recommended Workflow

1. Start from nucleotide FASTA queries and a valid PSSM domain database.
2. Set the query genetic code and strand explicitly when the biology is not generic nuclear DNA.
3. Emit tabular output with explicit fields for downstream parsing.
4. Interpret hits as conserved-domain evidence, not as full-length protein orthology by themselves.

Guardrails

• -db must be a PSSM/profile database, not a standard nucleotide or protein BLAST DB.
• Use -help rather than --help; --version errors in this BLAST+ build.
• -remote is incompatible with local threading.
• Translated domain searches can be noisy on raw contigs, so set -query_gencode, -strand, -outfmt, and -evalue deliberately.