There are many command line parameters that can be applied to a BLAST search to customize the results. Here are a few of the most commonly used parameters. For a complete listing please see the BLASTĀ® Command Line Applications User Manual.

DATABASE

DESCRIPTION

query Input file name
db Database being searched
out Output file name
query_loc Start and stop position in the query sequence to specify a shorter section of sequence to be searched. (Format: start-stop)
num_descriptions Number of one line descriptions of hits to report in the output file
num_alignments Number of alignments of hits to display in the output file
num_threads Number of threads (CPUs) to use in blast search