▁in ▁step ▁ 2 ▁with ▁all ▁the ▁ 3 - letter ▁words . ▁By ▁using ▁the ▁scoring ▁matrix ▁( subst itution ▁matrix ) ▁to ▁score ▁the ▁comparison ▁of ▁each ▁resid ue ▁pair , ▁there ▁are ▁ 2 0 ^ 3 ▁possible ▁match ▁scores ▁for ▁a ▁ 3 - letter ▁word . ▁For ▁example , ▁the ▁score ▁obtained ▁by ▁comparing ▁P Q G ▁with ▁P EG ▁and ▁P Q A ▁is ▁respectively ▁ 1 5 ▁and ▁ 1 2 ▁with ▁the ▁B L OS UM 6 2 ▁weight ing ▁scheme . ▁For ▁DNA ▁words , ▁a ▁match ▁is ▁scored ▁as ▁+ 5 ▁and ▁a ▁mismatch ▁as ▁- 4 , ▁or ▁as ▁+ 2 ▁and ▁- 3 . ▁After ▁that , ▁a ▁neighborhood ▁word ▁score ▁threshold ▁T ▁is ▁used ▁to ▁reduce ▁the ▁number ▁of ▁possible ▁matching ▁words . ▁The ▁words ▁whose ▁scores ▁are ▁greater ▁than ▁the ▁threshold ▁T ▁will ▁remain ▁in ▁the ▁possible ▁matching ▁words ▁list , ▁while ▁those ▁with ▁lower ▁scores ▁will ▁be ▁disc arded . ▁For ▁example , ▁P EG ▁is ▁kept , ▁but ▁P Q A ▁is ▁abandoned ▁when ▁T ▁is ▁ 1 3 . ▁ ▁Organ ize ▁the ▁remaining ▁high - sc oring ▁words ▁into ▁an ▁efficient ▁search ▁tree . ▁ ▁This ▁allows ▁the ▁program ▁to ▁rapidly ▁compare ▁the ▁high - sc oring ▁words ▁to ▁the ▁database ▁sequences . ▁ ▁Re peat ▁step ▁ 3 ▁to ▁ 4 ▁for ▁each ▁k - letter ▁word ▁in ▁the ▁query ▁sequence . ▁ ▁Sc an ▁the ▁database ▁sequences ▁for ▁exact ▁matches ▁with ▁the ▁remaining