Use when performing nucleotide-nucleotide similarity searches to identify homologs, annotate sequences, or compare query sequences against nucleotide databases.
blastn/home/vimalinx/miniforge3/envs/bio/bin/blastnreferences/help.mdblastn for genome fragments, amplicons, contigs, or transcript sequences.-task megablast for close matches and -task blastn-short for short primers or probes.tblastn instead when the query is protein and the target is nucleotide.# 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
-db) or a one-off FASTA subject (-subject).-task first, because it changes defaults and search behavior materially.-outfmt 6 or 7 unless you explicitly want pairwise text.-help rather than --help; BLAST+ distinguishes those forms.-db and -subject are mutually exclusive.megablast, which is fast but less sensitive for divergent homologs.-outfmt explicitly for reproducible downstream parsing.-remote changes execution mode and is usually not what you want for bulk local workflows.