Title :
Searching genetic databases on Splash 2
Author_Institution :
Dept. of Comput. Sci., Brown Univ., Providence, RI, USA
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
Keywords :
biology computing; logic arrays; reconfigurable architectures; special purpose computers; 12 million characters per second; Splash 2; database searching; dynamic programming algorithm; edit distance; genetic sequences; programmable logic array; systolic arrays; Concurrent computing; Cost function; Databases; Dynamic programming; Genetics; Heuristic algorithms; Integral equations; Programmable logic arrays; Sequences; Systolic arrays;
Conference_Titel :
FPGAs for Custom Computing Machines, 1993. Proceedings. IEEE Workshop on
Conference_Location :
Napa, CA
Print_ISBN :
0-8186-3890-7
DOI :
10.1109/FPGA.1993.279464
