▁in ▁order ▁to ▁find ▁matches . ▁The ▁threshold ▁score ▁T ▁determ ines ▁whether ▁or ▁not ▁a ▁particular ▁word ▁will ▁be ▁included ▁in ▁the ▁alignment . ▁Once ▁seed ing ▁has ▁been ▁conducted , ▁the ▁alignment ▁which ▁is ▁only ▁ 3 ▁resid ues ▁long , ▁is ▁extended ▁in ▁both ▁directions ▁by ▁the ▁algorithm ▁used ▁by ▁B LA ST . ▁Each ▁extension ▁impact s ▁the ▁score ▁of ▁the ▁alignment ▁by ▁either ▁increasing ▁or ▁decre asing ▁it . ▁If ▁this ▁score ▁is ▁higher ▁than ▁a ▁pre - det erm ined ▁T , ▁the ▁alignment ▁will ▁be ▁included ▁in ▁the ▁results ▁given ▁by ▁B LA ST . ▁However , ▁if ▁this ▁score ▁is ▁lower ▁than ▁this ▁pre - det erm ined ▁T , ▁the ▁alignment ▁will ▁ce ase ▁to ▁extend , ▁prevent ing ▁the ▁areas ▁of ▁poor ▁alignment ▁from ▁being ▁included ▁in ▁the ▁B LA ST ▁results . ▁Note ▁that ▁increasing ▁the ▁T ▁score ▁limits ▁the ▁amount ▁of ▁space ▁available ▁to ▁search , ▁decre asing ▁the ▁number ▁of ▁neighborhood ▁words , ▁while ▁at ▁the ▁same ▁time ▁speed ing ▁up ▁the ▁process ▁of ▁B LA ST ▁ ▁Algorithm ▁ ▁To ▁run ▁the ▁software , ▁B LA ST ▁requires ▁a ▁query ▁sequence ▁to ▁search ▁for , ▁and ▁a ▁sequence ▁to ▁search ▁against ▁( also ▁called ▁the ▁target ▁sequence ) ▁or ▁a ▁sequence ▁database ▁containing ▁multiple ▁such ▁sequences . ▁B LA ST ▁will ▁find ▁sub - sequ ences ▁in ▁the ▁database ▁which ▁are ▁similar ▁to ▁sub ▁sequences ▁in ▁the ▁query . ▁In ▁typical ▁usage , ▁the ▁query ▁sequence ▁is ▁much ▁smaller