A Protein Sequence Analysis Hardware Accelerator Based on Divergences

Table 7

Total system performance and obtained performance gains.

Sequence set elements	Number of HMM nodes	Prefilter hardware execution time (sec)	Divergence second-stage execution time (sec)	Total time (tsa(i,j))	Unaccelerated HMMER execution time (sec)	Obtained gain
687406	788	0.0971	0.0515	0.1486	23.40	157.4697
	10	0.0097	0.0009	0.0106	0.40	37.7358
	226	0.0291	0.0144	0.0435	6.55	150.5747
	337	0.0388	0.0217	0.0605	9.85	162.8099
	2295	0.2622	0.1639	0.4261	74.49	174.8181
	901	0.1068	0.0579	0.1647	26.32	159.8057
697407	788	0.0985	0.0535	0.152	24.34	160.1316
	10	0.0099	0.001	0.0109	0.47	43.1193
	226	0.0296	0.0147	0.0443	6.68	150.7901
	337	0.0394	0.0217	0.0611	9.88	161.7021
	2295	0.2660	0.1735	0.4395	78.87	179.4539
	901	0.1084	0.0606	0.169	27.55	163.0178
700218	788	0.0989	0.0537	0.1526	24.40	159.8952
	10	0.0099	0.0009	0.0108	0.42	38.8889
	226	0.0297	0.0149	0.0446	6.76	151.5695
	337	0.0396	0.0226	0.0622	10.26	164.9518
	2295	0.2671	0.1787	0.4458	81.23	182.2118
	901	0.1088	0.0603	0.1691	27.41	162.0934
712734	788	0.1007	0.0559	0.1566	25.42	162.3244
	10	0.0101	0.0009	0.011	0.42	38.1818
	226	0.0302	0.015	0.0452	6.82	150.885
	337	0.0403	0.0222	0.0625	10.09	161.44
	2295	0.2719	0.1784	0.4503	81.07	180.0355
	901	0.1108	0.0604	0.1712	27.46	160.3972