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blastn:tldr:c3f99

blastn: Search the remote non-redundant nucleotide database using a nucleotide query.

blastn

$ blastn -query ${query-fa} -db ${nt} -remote

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This command is using the program called blastn to perform a nucleotide-nucleotide BLAST search.

Here is the breakdown of the command and its options:

blastn: This is the command for the BLASTN program. It is used for comparing nucleotide sequences to find similar regions.
-query ${query-fa}: This specifies the query sequence file for the BLAST search. ${query-fa} is a placeholder that should be replaced with the actual path or name of the query sequence file in FASTA format.
-db ${nt}: This specifies the database to search against. ${nt} is another placeholder that should be replaced with the actual path or name of the nucleotide sequence database to use for the search. In this case, it seems to be using the variable nt, so it might be defined elsewhere in the script.
-remote: This option indicates that the BLAST search should be performed on a remote server instead of locally. The query sequence file and the database will be transferred over the network to the remote server for the search to be executed there.

In summary, this command is using the blastn program to perform a BLAST search using a query sequence file and a nucleotide sequence database. The search is being performed remotely on a server specified by the -remote option.

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.

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