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Help Home > Alignment Search > Running an Alignment Search > Running an Alignment Search

BLAST query page panel header: squery sequences BLAST query page panel header: search criteria Program Parameters BLAST query page panel header: organisms

The Alignment Query Page: Setting Program Parameters

BLAST query panel

In the Program Settings panel, you can set values for parameters used by the BLAST, BLAT, and BLASTZ programs. For a description of these parameters see:



Advanced options

BLAST query databases

For even more fine-tuning of algorithm parameters you can enter command line arguments in the "Advanced options" text-box to be used in running alignment jobs for each of BLAST, BLAT and BLASTZ.

If you click on Advanced options, you will get a detailed description of the command line arguments available for each program.