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

$ blastn -query ${query-fa} -subject ${subject-fa} -evalue ${1e-9}

try on your machine

The command you provided is not complete, but I can explain the parts that are present:

blastn: This is the command-line tool for running the BLAST nucleotide-nucleotide alignment algorithm.

-query ${query-fa}: This option specifies the query sequence file, here represented by a variable ${query-fa}. The ${query-fa} is likely a placeholder for the actual name or path of the query FASTA file that contains the sequences you want to search against the subject.

-subject ${subject-fa}: This option specifies the subject sequence file, represented by a variable ${subject-fa}. Similar to the query file, ${subject-fa} is a placeholder for the name or path of the subject FASTA file that you want to search in.

-evalue ${1e-9}: This option sets the e-value threshold for the BLAST search. The e-value represents the expected number of chance alignments that would achieve the given similarity score or better by random chance. In this case, the e-value is set to 1e-9, which is 0.000000001 or 1 in 1 billion chance.

Note: The values represented by ${query-fa} and ${subject-fa} should be replaced with the actual names or paths of the respective files you want to use in the command. Additionally, it seems that the value ${1e-9} is not correctly substituted and should also be replaced with the desired e-value threshold.

This explanation was created by an AI. In most cases those are correct. But please always be careful and never run a command you are not sure if it is safe.

back to the blastn tool