▁the ▁program ▁to ▁find ▁the ▁actual ▁significant ▁sequences ▁in ▁the ▁database , ▁so ▁they ▁should ▁be ▁filtered ▁out . ▁The ▁regions ▁will ▁be ▁marked ▁with ▁an ▁X ▁( prote in ▁sequences ) ▁or ▁N ▁( n uc le ic ▁acid ▁sequences ) ▁and ▁then ▁be ▁ignored ▁by ▁the ▁B LA ST ▁program . ▁To ▁filter ▁out ▁the ▁low - complex ity ▁regions , ▁the ▁SE G ▁program ▁is ▁used ▁for ▁protein ▁sequences ▁and ▁the ▁program ▁D UST ▁is ▁used ▁for ▁DNA ▁sequences . ▁On ▁the ▁other ▁hand , ▁the ▁program ▁X NU ▁is ▁used ▁to ▁mask ▁off ▁the ▁tan dem ▁repe ats ▁in ▁protein ▁sequences . ▁ ▁Make ▁a ▁k - letter ▁word ▁list ▁of ▁the ▁query ▁sequence . ▁ ▁Take ▁k = 3 ▁for ▁example , ▁we ▁list ▁the ▁words ▁of ▁length ▁ 3 ▁in ▁the ▁query ▁protein ▁sequence ▁( k ▁is ▁usually ▁ 1 1 ▁for ▁a ▁DNA ▁sequence ) ▁" sequ entially ", ▁until ▁the ▁last ▁letter ▁of ▁the ▁query ▁sequence ▁is ▁included . ▁The ▁method ▁is ▁illustrated ▁in ▁figure ▁ 1 . ▁ ▁List ▁the ▁possible ▁matching ▁words . ▁ ▁This ▁step ▁is ▁one ▁of ▁the ▁main ▁differences ▁between ▁B LA ST ▁and ▁FA ST A . ▁FA ST A ▁car es ▁about ▁all ▁of ▁the ▁common ▁words ▁in ▁the ▁database ▁and ▁query ▁sequences ▁that ▁are ▁listed ▁in ▁step ▁ 2 ; ▁however , ▁B LA ST ▁only ▁car es ▁about ▁the ▁high - sc oring ▁words . ▁The ▁scores ▁are ▁created ▁by ▁comparing ▁the ▁word ▁in ▁the ▁list