As mentioned previously, BLAST URLAPI commands take a variety of parameters. Different combinations of those parameters provide users with additional controls over their search request and formatting options.
For example, to search with short nucleotide queries, we often need to disable the low complexity filter and loosen the Expect cutoff so that we can see the short matches normally not reported by BLAST. We can accomplish this by using 'FILTER=F&EXPECT=1000'. Another example is searching with a human genomic query, there we need to activate the human repeat filter to mask the repeats present in the query and reduce the number of spurious matches to similar repeats found in the database. To do so, we will need to add another FILTER parameter 'FILTER=R'.