Table 1.

Memory footprint (in Bytes) required by the proposed COPS implementation, when compared with the original HMMER ViterbyFilter

Data structure	COPS (proposed)	ViterbiFilter
		(HMMER)
Mmx, Dmx, Imx	3×M×16	3×M×2
Transition scores	8×M×16	8×M×2
Emission match (E.M.) scores	M×16	M×2
Auxiliary emission array	24×16	–
∼20 aux. variables	20×16	20×16
Total	192×M+700	24×M+320
Total minus E.M. scores	176×M+700	22×M+320
Max. M to fill a 32 KB cache	$\frac{32768-700}{192}\approx 167$	$\frac{32768-320}{24}\approx 1350$

M represents the model length and all the computed scores are represented with 16-bit integers.