A Protein Sequence Analysis Hardware Accelerator Based on Divergences

Table 5

Hardware performance results.

Sequence set elements	Number of HMM nodes	25 PEs		50 PEs		75 PEs		85 PEs
		Thw (GCUPS)	th (sec)	Thw (GCUPS)	th (sec)	Thw (GCUPS)	th (sec)	Thw (GCUPS)	th (sec)
687406	788	1.7468	0.3101	3.4903	0.1552	4.9293	0.1068	5.4203	0.0971
	10	0.7093	0.0097	0.7086	0.0097	0.6880	0.0097	0.6877	0.0097
	226	1.6031	0.0969	3.2033	0.0485	3.8876	0.0388	5.1815	0.0291
	337	1.7075	0.1357	3.4118	0.0679	4.6377	0.0485	5.7949	0.0388
	2295	1.7695	0.8915	3.5358	0.4462	5.0942	0.3010	5.8468	0.2622
	901	1.7274	0.3586	3.3607	0.1843	4.7691	0.1262	5.6341	0.1068
697407	788	1.7468	0.3146	3.4904	0.1574	4.9295	0.1083	5.4205	0.0985
	10	0.7093	0.0098	0.7086	0.0098	0.6880	0.0099	0.6877	0.0099
	226	1.6031	0.0983	3.2033	0.0492	3.8878	0.0394	5.1817	0.0296
	337	1.7075	0.1376	3.4119	0.0689	4.6379	0.0492	5.7952	0.0394
	2295	1.7695	0.9045	3.5359	0.4527	5.0944	0.3053	5.8471	0.2660
	901	1.7274	0.3638	3.3608	0.1870	4.7693	0.1280	5.6344	0.1084
700218	788	1.7468	0.3159	3.4905	0.1581	4.9296	0.1088	5.4206	0.0989
	10	0.7093	0.0099	0.7086	0.0099	0.6880	0.0099	0.6877	0.0099
	226	1.6031	0.0987	3.2034	0.0494	3.8878	0.0396	5.1818	0.0297
	337	1.7075	0.1382	3.4120	0.0692	4.6379	0.0494	5.7953	0.0396
	2295	1.7695	0.9081	3.5359	0.4545	5.0945	0.3066	5.8472	0.2671
	901	1.7274	0.3652	3.3608	0.1877	4.7693	0.1286	5.6345	0.1088
712734	788	1.7468	0.3215	3.4906	0.1609	4.9298	0.1107	5.4209	0.1007
	10	0.7093	0.0100	0.7086	0.0101	0.6880	0.0101	0.6878	0.0101
	226	1.6031	0.1005	3.2035	0.0503	3.8880	0.0403	5.1821	0.0302
	337	1.7075	0.1407	3.4121	0.0704	4.6382	0.0503	5.7956	0.0403
	2295	1.7695	0.9244	3.5360	0.4626	5.0947	0.3120	5.8475	0.2719
	901	1.7274	0.3718	3.3609	0.1911	4.7696	0.1308	5.6348	0.1108