blastn

Align sequences using megablast with e-value threshold

$ blastn -query [query.fa] -subject [subject.fa] -evalue [1e-9]

$ blastn -task blastn -query [query.fa] -subject [subject.fa]

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

$ blastn -query [query.fa] -db [path/to/blast_db] -num_threads [16] -max_target_seqs [10]

$ blastn -query [query.fa] -db nt -remote

$ blastn -h

blastn [options]

blastn performs nucleotide-to-nucleotide BLAST (Basic Local Alignment Search Tool) searches. It finds regions of similarity between nucleotide sequences, which can indicate functional, structural, or evolutionary relationships.
The tool supports multiple search algorithms including megablast (default, for highly similar sequences), discontiguous megablast, and standard blastn. Results can help identify genes, compare genomes, or find homologous sequences.

-query file

Input file with query sequences in FASTA format

Subject sequence file for direct comparison

BLAST database name for searching

Expectation value (E) threshold for reporting matches

Algorithm variant: megablast, dc-megablast, or blastn

Output format (0=pairwise, 6=tabular, 7=tabular with headers)

Output file name

Number of CPU threads to use

Maximum number of aligned sequences to keep

Execute search on NCBI servers

Large database searches require significant memory and time. Remote searches are rate-limited. Local database searches require pre-formatted BLAST databases created with makeblastdb.

BLAST was developed at NCBI (National Center for Biotechnology Information) with the original algorithm published in 1990 by Altschul et al. It has become one of the most widely used bioinformatics tools.

blastp(1), blastx(1), makeblastdb(1)