The use of low-complexity masking in the BLAST procedure means that it may have higher specificity than FASTA because potential false positives are reduced.

Database similarity search is based upon sequence alignment methods also used in pairwise sequence comparison. Sequence alignment can be global (whole sequence alignment) or local (partial sequence alignment) and there are algorithms to find the optimal alignment given particular comparison criteria.

Topics include: Heuristic Database Searching, FASTA, Comparison of FASTA and BLAST, & Database Searching with the Smith – Waterman Method.