A Protein Sequence Analysis Hardware Accelerator Based on Divergences

Table 6

Second-stage performance estimations.

Sequence set elements	Number of HMM nodes	Entire sequence set processing time in unaccelerated HMMER (sec)	Significant sequences reprocessing time with prefilter and unaccelerated HMMER (sec)	Divergence accelerated significant sequences reprocessing time (sec)
687406	788	23.40	0.234	0.0515
	10	0.40	0.004	0.0009
	226	6.55	0.0655	0.0144
	337	9.85	0.0985	0.0217
	2295	74.49	0.7449	0.1639
	901	26.32	0.2632	0.0579
697407	788	24.34	0.2434	0.0535
	10	0.47	0.0047	0.001
	226	6.68	0.0668	0.0147
	337	9.88	0.0988	0.0217
	2295	78.87	0.7887	0.1735
	901	27.55	0.2755	0.0606
700218	788	24.40	0.244	0.0537
	10	0.42	0.0042	0.0009
	226	6.76	0.0676	0.0149
	337	10.26	0.1026	0.0226
	2295	81.23	0.8123	0.1787
	901	27.41	0.2741	0.0603
712734	788	25.42	0.2542	0.0559
	10	0.42	0.0042	0.0009
	226	6.82	0.0682	0.015
	337	10.09	0.1009	0.0222
	2295	81.07	0.8107	0.1784
	901	27.46	0.2746	0.0604