# Tblastx

> Use when searching nucleotide sequences against a nucleotide database using translated protein comparison. Useful for detecting distant evolutionary relationships between nucleotide sequences.

- Skill: `vimalinx/tblastx` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add vimalinx/tblastx`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/tblastx/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: vimalinx (https://skillmd.com/u/vimalinx)
- Updated: 2026-08-19
- Page: https://skillmd.com/skills/vimalinx/tblastx

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# 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

```bash
# 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
```

```bash
# 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
```

```bash
# 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.