, ▁a ▁vector ized ▁implementation ▁of ▁the ▁rig orous ▁Smith - W at erman ▁algorithm . ▁ ▁FA ST A ▁is ▁slower ▁than ▁B LA ST , ▁but ▁provides ▁a ▁much ▁wider ▁range ▁of ▁scoring ▁matrices , ▁making ▁it ▁easier ▁to ▁tail or ▁a ▁search ▁to ▁a ▁specific ▁evolution ary ▁distance . ▁ ▁An ▁extremely ▁fast ▁but ▁consider ably ▁less ▁sensitive ▁alternative ▁to ▁B LA ST ▁is ▁B L AT ▁( B last ▁Like ▁Al ignment ▁Tool ). ▁While ▁B LA ST ▁does ▁a ▁linear ▁search , ▁B L AT ▁re lies ▁on ▁k - mer ▁indexing ▁the ▁database , ▁and ▁can ▁thus ▁often ▁find ▁se eds ▁faster . ▁Another ▁software ▁alternative ▁similar ▁to ▁B L AT ▁is ▁Pattern H unter . ▁ ▁Adv ances ▁in ▁sequ encing ▁technology ▁in ▁the ▁late ▁ 2 0 0 0 s ▁has ▁made ▁searching ▁for ▁very ▁similar ▁nucle ot ide ▁matches ▁an ▁important ▁problem . ▁New ▁alignment ▁programs ▁tail ored ▁for ▁this ▁use ▁typically ▁use ▁B WT - index ing ▁of ▁the ▁target ▁database ▁( typ ically ▁a ▁gen ome ). ▁Input ▁sequences ▁can ▁then ▁be ▁mapped ▁very ▁quickly , ▁and ▁output ▁is ▁typically ▁in ▁the ▁form ▁of ▁a ▁B AM ▁file . ▁Example ▁alignment ▁programs ▁are ▁B WA , ▁SO AP , ▁and ▁Bow t ie . ▁ ▁For ▁protein ▁identification , ▁searching ▁for ▁known ▁domains ▁( for ▁instance ▁from ▁Pf am ) ▁by ▁matching ▁with ▁H idden ▁Mark ov ▁Mod els ▁is ▁a ▁popular ▁alternative , ▁such ▁as ▁H MM ER . ▁ ▁An