Sequence Alignment and Similarity Search:
Database similarity searching
allows us to determine which of the hundreds of thousands of sequences present
in the database are potentially related to a particular sequence of interest.
In database searching, the basic operation is to sequentially align a query sequence to each subject sequence in the database. The results
are reported as a ranked hit list followed by a series of individual sequence
alignments, plus various scores and statistics. Current sequence databases are
already immense and have continued to increase at an exponential rate, making
straightforward application of dynamic programming methods impractical for
database searching. One solution is to use massively parallel computers. There
are several frequently used programs available on the Internet: