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

Table 2

Performance comparison for different numbers of threads per block (64, 128, 256). All query sequences run against the SWISS-PROT database [18].

Query length	Thread 64	Thread 128	Thread 256
	time (sec)	time (sec)	time (sec)
63	2.1	3.1	6.2
127	6.1	4.2	7.2
191	9.3	11.9	8.3
255	12.5	12.9	9.6
511	25.1	26.4	29.2
1023	50.4	53.1	57.8