A Protein Sequence Analysis Hardware Accelerator Based on Divergences

Table 4

Modified hmmsearch performance results.

Sequence set elements	Number of HMM nodes	Measured time (total)	Measured time (Viterbi only)	Estimated time (Viterbi only)	Error (%)
687406	788	23.40	23.28	22.871	1.75
	10	0.40	0.35	0.1810	48.2
	226	6.55	6.47	6.5635	1.42
	337	9.85	9.8	9.8199	0.2
	2295	74.49	64.09	64.6425	0.8
	901	26.32	26.25	26.1199	0.4
697407	788	24.34	23.48	23.2158	1.12
	10	0.47	0.41	0.1853	54.1
	226	6.68	6.66	6.6602	0.003
	337	9.88	9.83	9.9634	1.35
	2295	78.87	62.89	65.5334	4.2
	901	27.55	25.96	26.4938	2.05
700218	788	24.40	23.37	23.3082	0.264
	10	0.42	0.38	0.1865	50.92
	226	6.76	6.72	6.6873	0.486
	337	10.26	9.84	10.0037	1.663
	2295	81.23	62.25	65.7849	5.678
	901	27.41	26.33	26.5989	1.021
712734	788	25.42	24.03	23.7193	1.293
	10	0.42	0.37	0.1919	48.13
	226	6.82	6.77	6.8083	0.565
	337	10.09	10.01	10.1832	1.730
	2295	81.07	63.81	66.8985	4.840
	901	27.46	26.82	27.0665	0.919

*Execution times are all expressed in seconds.