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Table 4 Comparison of RNAspa with RNAcast using different RNAcast parameters

From: RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules

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
  1. 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.