BLAST vs FASTA
FASTA - a sensitive search engine
The early personal computers had insufficient memory and were too slow to carry out a database scan using a rigorous searching method (dynamic programming). Accordingly, Wilbur and Lipman [(1983) Proc. Nat. Acad. Sci. 80, 726-730] developed a fast procedure for DNA scans that in concept searches for the most significant diagonals in a dot plot. FASTA only shows the top scoring region, it does not locate all high scoring alignments between two sequences. As a consequence, FASTA may not directly identify repeats or multiple domains that are shared between two proteins
BLAST - a faster alternative
BLAST (Basic Local Alignment Search Tool) is a heuristic method to find the highest scoring locally optimal alignments between a query sequence and a database. Previous versions of BLAST did not allow gapped alignments, but BLAST2 (from the HGMP-RC telnet and www menus) does. A gapped BLAST search allows gaps (deletions and insertions) to be introduced into the alignments that are returned. Allowing gaps means that similar regions are not broken into several segments. The scoring of these gapped alignments tends to reflect biological relationships more closely.