- Basic Local Alignment Search Tool. The Basic Local Alignment Search Tool (BLAST) is an algorithm that finds regions of local similarity between amino-acid or nucleotide sequences. A BLAST search enables you to compare a query sequence with a library or database of sequences, identifying sequences in the database that resemble the query sequence above a certain threshold. For example, use BLAST to search for a gene sequence in a whole genome. The basic local alignment tool uses heuristics (rules of thumb) to decrease the search time. It searches for matching words of a specific length and then extends them until it hits a mismatch.