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.