This program lets you enter not only the query for your blast search but also the database you want to blast against. This can be quite useful if you want to blast against some DNA sequences like oligos or your own reads but you don't have them formatted as a blast database.
Moreover, if your query is only one sequence and this sequence is a DNA sequence, then you can select "Artemis" as an Alignment view in the Advanced Options section below. Then your blast results will be shown in the neat program Artemis. It will be opened with your query as sequence and the blast hits will be the annotation for it.
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