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On this page you find all important commands for the CLI tool blastn. If the
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blastn
- blastn is a command line tool used for sequence alignment and comparative genomics analysis.
- It is a part of the Basic Local Alignment Search Tool (BLAST) suite of tools.
- The primary purpose of blastn is to compare nucleotide sequences (DNA or RNA) against a specified reference database.
- It can be used to identify similar sequences, search for homologous genes, and analyze evolutionary relationships.
- blastn uses an algorithm called the "BLAST algorithm" to perform sequence alignment.
- It measures the similarity between two sequences by calculating a sequence alignment score and an E-value (a measure of statistical significance).
- The output of blastn includes a list of significant matches, sequence alignments, and statistical information.
- It supports various input formats, including plain text, FASTA, and GenBank.
- blastn provides various options to customize the search parameters and improve sensitivity or speed, depending on the requirements.
- 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:
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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 ${10}try on your machineexplain this command
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blastn:tldr:1dc78 blastn: Align two or more sequences using megablast (default), with the e-value threshold of 1e-9, pairwise output format (default).$ blastn -query ${query-fa} -subject ${subject-fa} -evalue ${1e-9}try on your machineexplain this command
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blastn:tldr:c0c63 blastn: Display help (use `-help` for detailed help).$ blastn -htry on your machineexplain this command
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blastn:tldr:c3f99 blastn: Search the remote non-redundant nucleotide database using a nucleotide query.$ blastn -query ${query-fa} -db ${nt} -remotetry on your machineexplain this command
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blastn:tldr:cae83 blastn: Align two or more sequences, custom tabular output format, output to file.$ blastn -query ${query-fa} -subject ${subject-fa} -outfmt ${'6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident'} -out ${output-tsv}try on your machineexplain this command
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blastn:tldr:e9af8 blastn: Align two or more sequences using blastn.$ blastn -task blastn -query ${query-fa} -subject ${subject-fa}try on your machineexplain this command