A Systolic Array-Based FPGA Parallel Architecture for the BLAST Algorithm

Table 4

Execution time of our architecture and software versions.

Query length	BLASTp		TBLASTn		BLASTx		TBLASTx
	ST(ms)	HT(ms)	ST(ms)	HT(ms)	ST(ms)	HT(ms)	ST(ms)	HT(ms)
128	1901	1050	3203	153	1594	1030	4031	163
256	3087	1058	3641	167	2641	1042	5906	198
512	5603	1092	5156	202	4378	1074	9978	270
1 K	9327	1150	9891	254	7828	1135	16266	351
2 K	17814	1220	15438	360	13187	1210	27703	462
3 K	25132	1490	20328	436	18875	1331	37500	536