Forrest logo
tool overview
On this page you find all important commands for the CLI tool blastn. If the command you are looking for is missing please ask our AI.

blastn

  1. blastn is a command line tool used for sequence alignment and comparative genomics analysis.
  2. It is a part of the Basic Local Alignment Search Tool (BLAST) suite of tools.
  3. The primary purpose of blastn is to compare nucleotide sequences (DNA or RNA) against a specified reference database.
  4. It can be used to identify similar sequences, search for homologous genes, and analyze evolutionary relationships.
  5. blastn uses an algorithm called the "BLAST algorithm" to perform sequence alignment.
  6. It measures the similarity between two sequences by calculating a sequence alignment score and an E-value (a measure of statistical significance).
  7. The output of blastn includes a list of significant matches, sequence alignments, and statistical information.
  8. It supports various input formats, including plain text, FASTA, and GenBank.
  9. blastn provides various options to customize the search parameters and improve sensitivity or speed, depending on the requirements.
  10. It is widely used in bioinformatics and genomics research for tasks like genome annotation, identifying pathogens, and comparing gene expression.

List of commands for blastn:

  • blastn:tldr:036f3 blastn: 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}
    try on your machine
    explain this command
  • blastn:tldr:1dc78 blastn: 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}
    try on your machine
    explain this command
  • blastn:tldr:c0c63 blastn: Display help (use `-help` for detailed help).
    $ blastn -h
    try on your machine
    explain this command
  • blastn:tldr:c3f99 blastn: Search the remote non-redundant nucleotide database using a nucleotide query.
    $ blastn -query ${query-fa} -db ${nt} -remote
    try on your machine
    explain this command
  • blastn:tldr:cae83 blastn: 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}
    try on your machine
    explain this command
  • blastn:tldr:e9af8 blastn: Align two or more sequences using blastn.
    $ blastn -task blastn -query ${query-fa} -subject ${subject-fa}
    try on your machine
    explain this command
tool overview