deltablast

name	deltablast
description	Use when performing domain-enhanced protein sequence similarity searches to detect remote homologs using conserved domain databases.
disable-model-invocation	true
user-invocable	true

deltablast

Quick Start

• Command: deltablast
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/deltablast
• Version: 2.17.0+
• Full reference: See references/help.md

When To Use This Tool

• Search protein queries for distant homologs when ordinary blastp is not sensitive enough.
• Leverage conserved-domain hits to seed a PSSM before searching a protein database.
• Save PSSMs for later inspection or reuse in iterative workflows.
• Prefer ordinary blastp for straightforward close homolog searches and psiblast when you want fully iterative profile refinement.

Common Patterns

# 1) Domain-enhanced search against a protein database
deltablast \
  -query query.fa \
  -db prot_db \
  -rpsdb cdd_delta \
  -outfmt "6 qaccver saccver pident length evalue bitscore qcovhsp" \
  -evalue 1e-3 \
  -max_target_seqs 20 \
  -num_threads 8

# 2) Save the generated PSSM for downstream inspection
deltablast \
  -query query.fa \
  -db prot_db \
  -rpsdb cdd_delta \
  -num_iterations 2 \
  -out_pssm query.pssm

# 3) Tighten sequence and domain inclusion thresholds
deltablast \
  -query query.fa \
  -db prot_db \
  -rpsdb cdd_delta \
  -inclusion_ethresh 1e-4 \
  -domain_inclusion_ethresh 1e-3

Recommended Workflow

1. Start with protein queries and confirm that both the target protein database and the RPS domain database are available locally.
2. Save machine-readable output and, when useful, the generated PSSM.
3. Tune inclusion thresholds and iteration count only after examining the first-pass behavior.
4. Compare suspicious results to a plain blastp run so the domain enhancement is actually helping.

Guardrails

• DELTA-BLAST expects protein queries and protein search databases.
• -rpsdb is central to the method and is incompatible with -remote and -subject in this build.
• -num_iterations is not available with -remote.
• Use -help rather than --help; --version also errors here.