Searching genetic databases on Splash 2

Abstract

The author describes two systolic arrays for computing the edit distance between two genetic sequences using a well-known dynamic programming algorithm. The systolic arrays have been implemented for the Splash 2 programmable logic array and are intended to be used for database searching. Simulations indicate that the faster Splash 2 implementation can search a database at a rate of 12 million characters per second, several orders of magnitude faster than implementations of the dynamic programming algorithm on conventional computers.<>