The filter option, if set to true, when running a blast, will allow you to mask out various segments of the query sequence for regions which are non-specific for sequence similarity searches. Filtering can eliminate statistically significant but biologically uninteresting reports from the output, for example hits against common acidic-, basic- or proline-rich regions, leaving the more biologically interesting regions of the query sequence available for specific matching against database sequences. Filtering is only applied to the query sequence, not to database sequences. The program used for this, with nucleotide query sequences is known as DUST written by Tatusov, R. L., and Lipman, D.J. The SEG program is used for filtering low complexity regions in amino acid sequences from your protein query sequence and was written by Wootton, J.C., and Federhen, S.