High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

Table 3

Performance comparison. All query sequences run against the SWISS-PROT database.

Query (protein name)	Query length	FPGA; time (sec)	GPU; time (sec)	Cell BE; time (sec)	GPP; time (sec)
P36515	4	1.5	4.1	0.5	24
P81780	8	1.6	4.1	1.0	30
P83511	16	1.6	4.3	1.3	43
O19927	32	1.6	4.7	1.4	62
A4T9V0	64	1.6	6.7	2.5	115
Q2IJ63	128	1.6	12.8	5.1	210
P28484	256	1.9	30.0	9.4	424
Q1JLB7	512	4.5	76	17.2	779
A2Q8L1	768	6.7	136.2	22.2	1356
P08715	1024	8.9	172.8	31.8	1817