blastn

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

Install

All systems
curl cmd.cat/blastn.sh
Debian Debian
apt-get install ncbi-blast+
Ubuntu
apt-get install ncbi-blast+
image/svg+xml Kali Linux
apt-get install ncbi-blast+
Fedora
dnf install ncbi-blast+
Windows (WSL2)
sudo apt-get update sudo apt-get install ncbi-blast+
OS X
brew install blast
Raspbian
apt-get install ncbi-blast+
Dockerfile
dockerfile.run/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

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