blastn:tldr:e9af8

The command "blastn" is a general command for running the BLASTN program, which is used for nucleotide-nucleotide sequence comparisons. Here is the breakdown of the components:

• "blastn" is the command itself, indicating that we want to run the BLASTN program.
• "-task blastn" specifies that BLASTN will be used as the algorithm for sequence comparison. This is redundant because we are already running the "blastn" command, but it explicitly specifies the task to avoid any ambiguity.
• "-query ${query-fa}" specifies the input query sequence file. "${query-fa}" refers to a variable or file name that contains the path to the query FASTA file. FASTA is a common file format for storing nucleotide or protein sequences.
• "-subject ${subject-fa}" specifies the input subject sequence or database file. "${subject-fa}" refers to a variable or file name that contains the path to the subject FASTA file. In BLASTN, the subject sequence is the target against which the query sequence is compared.

To use this command properly, you need to replace "${query-fa}" and "${subject-fa}" with the actual file paths to your query and subject FASTA files, respectively. Additionally, you may need to make sure that the BLASTN program is properly installed and accessible in your system's PATH environment variable.