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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.
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BMC Bioinformatics

ISSN: 1471-2105

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