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blastn — Nucleotide-Nucleotide BLAST. More information: <https://www.ncbi.nlm.nih.gov/books/NBK279684/table/a

Submitted by: @import:tldr-pages·Mar 2, 2026·

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Problem

How to use the blastn command: Nucleotide-Nucleotide BLAST. More information: <https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.blastn_application_options/>.

Solution

blastn — Nucleotide-Nucleotide BLAST. More information: <https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.blastn_application_options/>.

Align two or more sequences using megablast (default), with the e-value threshold of 1e-9, pairwise output format (default):

blastn -query {{query.fa}} -subject {{subject.fa}} -evalue {{1e-9}}

Align two or more sequences using blastn:

blastn -task blastn -query {{query.fa}} -subject {{subject.fa}}

Align two or more sequences, custom tabular output format, output to file:

blastn -query {{query.fa}} -subject {{subject.fa}} -outfmt '{{6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident}}' -out {{output.tsv}}

Search nucleotide databases using a nucleotide query, 16 threads (CPUs) to use in the BLAST search, with a maximum number of 10 aligned sequences to keep:

blastn -query {{query.fa}} -db {{path/to/blast_db}} -num_threads {{16}} -max_target_seqs {{10}}

Search the remote non-redundant nucleotide database using a nucleotide query:

blastn -query {{query.fa}} -db {{nt}} -remote

Display help (use -help for detailed help):

blastn -h

Code Snippets

Align two or more sequences using megablast (default), with the e-value threshold of 1e-9, pairwise output format (default)

blastn -query {{query.fa}} -subject {{subject.fa}} -evalue {{1e-9}}

Align two or more sequences using blastn

blastn -task blastn -query {{query.fa}} -subject {{subject.fa}}

Align two or more sequences, custom tabular output format, output to file

blastn -query {{query.fa}} -subject {{subject.fa}} -outfmt '{{6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident}}' -out {{output.tsv}}

Search nucleotide databases using a nucleotide query, 16 threads (CPUs) to use in the BLAST search, with a maximum number of 10 aligned sequences to keep

blastn -query {{query.fa}} -db {{path/to/blast_db}} -num_threads {{16}} -max_target_seqs {{10}}

Search the remote non-redundant nucleotide database using a nucleotide query

blastn -query {{query.fa}} -db {{nt}} -remote

Context

tldr-pages: linux/blastn

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