tblastx

Quick Start

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

When To Use This Tool

• Compare nucleotide queries against nucleotide targets at the translated-protein level.
• Detect coding-region homology between divergent nucleotide sequences when blastn is too insensitive.
• Compare transcripts, contigs, or coding fragments across distant taxa.
• Prefer blastn for close nucleotide homology and blastx or tblastn when only one side should be translated.

Common Patterns

# 1) Standard translated-vs-translated search against a nucleotide BLAST database
tblastx \
  -query transcripts.fa \
  -db nt_db \
  -outfmt "6 qaccver saccver pident length evalue bitscore qcovhsp frames" \
  -evalue 1e-5 \
  -max_target_seqs 20 \
  -num_threads 8

# 2) One-off query-vs-subject comparison with explicit genetic codes
tblastx \
  -query transcripts.fa \
  -subject targets.fa \
  -query_gencode 11 \
  -db_gencode 11 \
  -outfmt 7

# 3) Restrict query orientation when strand is known
tblastx \
  -query transcripts.fa \
  -db nt_db \
  -strand plus \
  -outfmt 6

Recommended Workflow

1. Confirm that both query and target data are nucleotide and biologically expected to contain coding signal.
2. Decide whether the target is a BLAST database or a one-off FASTA subject.
3. Set -query_gencode and -db_gencode explicitly when organellar or nonstandard codes are plausible.
4. Treat hits as translated coding evidence and validate them with ORF-aware or annotation-aware follow-up tools.

Guardrails

• Both query and target must be nucleotide sequences.
• -db and -subject are mutually exclusive.
• tblastx is computationally expensive because both sides are translated in six frames.
• Use -help rather than --help; --version also errors in this BLAST+ build.
• -remote is incompatible with local threading.