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 BLAST® Command Line Applications User Manual.
|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|