BLAST

BLAST is the Basic Local Alignment Search Tool. The full paper is here.

$BLAST(db, seq)$ searches $db$ for sequences that are close matches to $seq$. $BLAST$ returns sequences matches ranked by percent identity, the percentage of identical elements in the sequence for the alignments. The score is then compared to the expected score (E-value) of searching a random database for $seq$, to determine statistical significance.