---
title: Query options reference
description: 'Set -evalue and -word_size to trade sensitivity against speed, cap -max_target_seqs, and pick an outfmt — tabular 6, JSON 15, or SAM-like 17.'
---

Tune what a [BLAST](/docs/blast) run reports and how it trades sensitivity against speed. The `-evalue` and `-word_size` flags most affect the result — they set how significant a hit must be to survive and how the sensitivity-versus-speed balance falls.

> **Where these commands run**

> You cannot open a shell on the platform yourself. The commands on this page are BLAST+ command lines: ask Ivy in chat to run them in the chat's [code workspace](/docs/sandbox), which ships BLAST+, or run them on your own machine. For a hosted search with no commands, see the [BLAST quickstart](/docs/blast/quickstart).

## Core flags (blastn example)

```bash
blastn \
  -query inputs/query.fasta \
  -db inputs/db/genomes_v1 \
  -num_threads 8 \
  -evalue 1e-5 \
  -max_target_seqs 10 \
  -perc_identity 85 \
  -dust yes \
  -outfmt "6 qseqid sseqid pident length mismatch gapopen evalue bitscore"
```

## Useful outfmt presets

- Tabular with comments: `-outfmt "7 std qcovs"`
- JSON (blast 2.14+): `-outfmt 15`
- SAM-like (BLASTN only): `-outfmt 17`

Log the selected `outfmt` and keep a sample row in your output summary.

## Controlling sensitivity vs. speed

- Increase sensitivity: lower `-word_size`, raise `-reward`, or reduce
  `-gapopen/-gapextend`.
- Increase speed: increase `-word_size`, cap `-max_target_seqs`, and raise
  `-evalue`.
- For protein searches, tune `-seg` (masking) and choose the right matrix
  (`-matrix BLOSUM62` is a safe default).

## Reproducibility checklist

- Pin BLAST+ version.
- Log command-line flags and database checksums.
- Persist stdout/stderr to `outputs/run.log`.
- Store the original query FASTA along with the results.

## Canvas Visualization

When a BLAST job completes, a result card appears on the canvas.

- **Card size**: 450x350px
- **Border color**: Brown (#795548)
- **Visualization**: Alignment data table

### Tier 2 Metrics

- Hit count
- Best E-value
- Best identity percentage
- Top hit description

### Key Thresholds

| Metric | Threshold | Interpretation |
|--------|-----------|---------------|
| E-value | < 1e-5 | Statistically significant hit |
| E-value | < 1e-50 | Strong homolog |
| Identity | > 30% | Same fold family (for proteins) |
| Identity | > 80% | Closely related sequences |
| Query coverage | > 70% | Good alignment coverage |