Table 4.

Comparison of RNAspa with RNAcast using different RNAcast parameters

Family	Avg. sequence identity	MCC
		RNAspa	RNAcast
			-t 5 -c 10 (default)	-t 5 -c 20	-t 3 -c 10	-t 3 -c 20
lin4	66%	0.86	0.73	0.73	no data	0.72
tRNA	50%	0.81	0.42	0.42	no data	0.65
5S RNA	59%	0.58	0.62	0.62	no data	0.84
U2	78%	0.74	0.72	0.72	0.69	0.69
S box riboswitch	67%	0.75	0.69	0.69	0.78	0.78
SRP RNA	52%	0.95	0.99	0.99	0.94	0.94
IRES	66%	0.97	0.93	0.93	0.90	0.90
Purine riboswitch	56%	0.93	0.78	0.78	0.81	0.81
U1	65%	0.67	0.72	0.72	no data	0.76
U12	83%	0.76	0.50	0.50	no data	0.68

RNAcast was run using four different configurations. RNAcast parameters that were used: -t sets the shape type (default: 5). Shape type defines the level of abstraction from most accurate to most abstract (1–5). -c sets the energy range (default: 10%). For seven out the ten families RNAspa gave better results. See [Additional File 7] for raw data.