Query options reference

Tune what a 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.

Core flags (blastn example)

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