rpsblast

name	rpsblast
description	Use when searching protein sequences against conserved domain databases like CDD using reverse position-specific BLAST
disable-model-invocation	true
user-invocable	true

rpsblast

Quick Start

• Command: rpsblast -query <input> -db <rpsdb> -out <output> -outfmt 6
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/rpsblast
• Version: 2.17.0+
• Full reference: See references/help.md

When To Use This Tool

• Annotate protein queries against conserved-domain PSSM databases such as CDD.
• Detect domain composition and family membership in predicted proteins.
• Prefer rpsblast when the target is a reverse-position-specific domain database, not a general protein sequence database.
• Prefer deltablast when you want domains to seed a PSSM and then search a protein database.

Common Patterns

# 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

Recommended Workflow

1. Confirm the query set is protein and the target database is an RPS/PSSM database.
2. Save machine-readable output with explicit columns.
3. Interpret domain calls in the context of whole-domain architecture, not just the top single domain hit.
4. Compare odd results to hmmscan or deltablast when the database or sensitivity assumptions differ.

Guardrails

• The query must be protein, and -db must point to an RPS/PSSM domain database rather than a standard BLAST protein DB.
• Use -help rather than --help; --version also errors in this BLAST+ build.
• -remote is incompatible with local threading.
• Set -outfmt, -evalue, and -max_target_seqs explicitly for reproducible annotation pipelines.