blastn

linux

Nucleotide-Nucleotide BLAST.

Examples (6)

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

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