blastn

name	blastn
description	Use when performing nucleotide-nucleotide similarity searches to identify homologs, annotate sequences, or compare query sequences against nucleotide databases.
disable-model-invocation	true
user-invocable	true

blastn

Quick Start

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

When To Use This Tool

• Search nucleotide queries against nucleotide databases.
• Prefer blastn for genome fragments, amplicons, contigs, or transcript sequences.
• Use -task megablast for close matches and -task blastn-short for short primers or probes.
• Use tblastn instead when the query is protein and the target is nucleotide.

Common Patterns

# 1) Standard local database search with tabular output
blastn \
  -query query.fa \
  -db nt_db \
  -outfmt "6 qaccver saccver pident length qstart qend sstart send evalue bitscore" \
  -evalue 1e-10 \
  -max_target_seqs 20 \
  -num_threads 8

# 2) Primer or short oligo search
blastn \
  -task blastn-short \
  -query primers.fa \
  -db nt_db \
  -word_size 7 \
  -outfmt 6

# 3) Query-vs-subject search without a prebuilt BLAST database
blastn \
  -query query.fa \
  -subject subject.fa \
  -outfmt 7

Recommended Workflow

1. Decide whether you are searching a local BLAST database (-db) or a one-off FASTA subject (-subject).
2. Set -task first, because it changes defaults and search behavior materially.
3. Emit machine-readable output with -outfmt 6 or 7 unless you explicitly want pairwise text.
4. Interpret hits using e-value, percent identity, query coverage, and biological context together.

Guardrails

• Use -help rather than --help; BLAST+ distinguishes those forms.
• -db and -subject are mutually exclusive.
• The default task is megablast, which is fast but less sensitive for divergent homologs.
• Always specify -outfmt explicitly for reproducible downstream parsing.
• -remote changes execution mode and is usually not what you want for bulk local workflows.