BLAST

Break probe and database into "words"
Initial search for all words of length W and score of at least T (using a substitution matrix)
Extend word hits in each direction while score exceeds threshold S
p-value : probability of seeing a score this good by relating S to expected distribution of scores from same length and composition probe
e-value : Number of alignments with scores this good expected to occur by chance

Break probe and database into "words"