blastx

Quick Start

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

When To Use This Tool

• Search nucleotide queries against protein databases by translating the query in six frames.
• Annotate transcripts, contigs, ORF candidates, or metagenomic nucleotide fragments against known proteins.
• Prefer blastp if the query is already protein, or tblastn if the query is protein and the target is nucleotide.
• Use -task blastx-fast when you want speed over maximum sensitivity.

Common Patterns

# 1) Standard translated search with tabular output
blastx \
  -query contigs.fa \
  -db prot_db \
  -outfmt "6 qaccver saccver pident length qstart qend sstart send evalue bitscore qcovhsp frames" \
  -evalue 1e-5 \
  -max_target_seqs 20 \
  -num_threads 8

# 2) Faster search mode for large screens
blastx \
  -task blastx-fast \
  -query contigs.fa \
  -db prot_db \
  -outfmt 6

# 3) One-off translated search against a protein FASTA subject and a nonstandard code
blastx \
  -query contigs.fa \
  -subject proteins.fa \
  -query_gencode 11 \
  -outfmt 7

Recommended Workflow

1. Confirm the query FASTA is nucleotide and the target is protein, either as a BLAST DB or a one-off subject FASTA.
2. Set -task and -query_gencode deliberately before comparing output across projects.
3. Emit tabular output with explicit fields for pipelines.
4. Interpret hits using e-value, coverage, frame, and biological plausibility together.

Guardrails

• -db and -subject are mutually exclusive.
• Use -help rather than --help; --version also errors in this BLAST+ build.
• Translated searches are expensive and can explode into many HSPs, so set -outfmt, -evalue, and -max_target_seqs explicitly.
• -remote changes execution semantics and is incompatible with local threading.